DNA time machine sheds light on lake

Image: Jordan Gonzalez, Unsplash

Scientists have run the first trials of a DNA ‘time machine’ designed to shed light on a century of environmental change in a freshwater lake.

Their approach uses artificial intelligence (AI) applied to DNA-based biodiversity, climate and pollution data, and could help regulators protect the planet’s existing biodiversity levels, or even improve them. Researchers from the University of Birmingham, UK, in collaboration with Goethe University in Frankfurt, Germany, used sediment from the bottom of a lake in Denmark to reconstruct a 100-year-old library of biodiversity, chemical pollution and climate change levels.

The lake has a history of well-documented shifts in water quality, making it a perfect natural experiment for testing the biodiversity time machine. Publishing their findings in journal eLife, the researchers reveal that the sediment holds a continuous record of biological and environmental signals that have changed over time - from pristine environments at the start of the industrial revolution to the present.

"These actions can help us not only to preserve the biodiversity we have today but potentially to improve biodiversity recovery."

Luisa Orsini, University of Birmingham

The team used environmental DNA - genetic material left behind by plants, animals and bacteria - to build a picture of the entire freshwater community. Assisted by AI, they analysed the information to identify what could explain the historic loss of species that lived in the lake.

Principal investigator Luisa Orsini, professor at the University of Birmingham said, “We took a sediment core from the bottom of the lake and used biological data within that sediment like a time machine - looking back in time to build a detailed picture of biodiversity over the last century at yearly resolution.

“By analysing biological data with climate change data and pollution levels we can identify the factors having the biggest impact on biodiversity. Protecting every species without impacting human production is unrealistic, but using AI we can prioritise the conservation of species that deliver ecosystem services.

"At the same time, we can identify the top pollutants, guiding regulation of chemical compounds with the most adverse effect. These actions can help us not only to preserve the biodiversity we have today, but potentially to improve biodiversity recovery.

"Biodiversity sustains many ecosystem services that we all benefit from. Protecting biodiversity mean protecting these services.”

Image: Joshua J. Cotten, Unsplash

Studies found that pollutants such as insecticides and fungicides, alongside increases in minimum temperature caused the most damage to biodiversity levels.

However, the DNA present in the sediment also showed that over the last 20 years the water quality had begun to recover, as agricultural land use declined in the area surrounding the lake. Yet, whereas the overall biodiversity increased, some lost species had not returned.

Niamh Eastwood, lead author and PhD student at the University of Birmingham said, “The biodiversity loss caused by this pollution and the warming water temperature is potentially irreversible.

“It is not possible to restore the lake to its original pristine state, even though the lake is recovering. This research shows that if we fail to protect biodiversity, much of it could be lost forever.”

Jiarui Zhou, co-lead author and assistant professor at the University of Birmingham said, “Learning from the past, our holistic models can help us to predict the likely loss of biodiversity under a ‘business as usual’ and other pollution scenarios.

"We have demonstrated the value of AI-based approaches for understanding historic drivers of biodiversity loss. As new data becomes available, more sophisticated AI models can be used to further improve our predictions of the causes of biodiversity loss.”

Next, the researchers are expanding their study to lakes in England and Wales to help them understand how replicable the patterns they observed in Denmark are.