'Biodiversity time machine' provides insights into a century of loss

Scientists have run the first proof of concept of their DNA 'time machine' to shed light on a century of environmental change in a freshwater lake -- including warming temperatures and pollution, leading to the potentially irreversible loss of biodiversity.

Their approach, which uses AI applied to DNA-based biodiversity, climate variables and pollution, could help regulators to protect the planet's existing biodiversity levels, or even improve them.

Researchers from the University of Birmingham, in collaboration with Goethe University in Frankfurt, 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. This 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 today (7 Nov) in eLife, the experts reveal that the sediment holds a continuous record of biological and environmental signals that have changed over time -- from (semi)pristine environments at the start of the industrial revolution to the present.

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, in conjunction with climate and pollution data, to identify what could explain the historic loss of species that lived in the lake.

Principal investigator Luisa Orsini, Professor of Evolutionary Systems Biology and Environmental Omics at the University of Birmingham and Fellow of the Alan Turing Institute, explained: "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."

The researchers found that pollutants such as insecticides and fungicides, alongside increases in minimum temperature (a 1.2-1.5-degree increase) caused the most damage to biodiversity levels.

However, the DNA present in the sediment also showed that over the last 20 years the lake had begun to recover. Water quality improved as agricultural land use declined in the area surrounding the lake. Yet, whereas the overall biodiversity increased, the communities were not the same as in the (semi)pristine phase. This is concerning as different species can deliver different ecosystem services, and therefore their inability to return to a particular site can prevent the reinstatement of specific services.

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. The species found in the lake 100 years ago that have been lost will not all be able to return. 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."

Dr Jiarui Zhou, co-lead author and Assistant Professor in Environmental Bioinformatics 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."

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Half of world's largest lakes losing water

More than 50 percent of the largest lakes in the world are losing water, according to a groundbreaking new assessment published today in Science . The key culprits are not surprising: warming climate and unsustainable human consumption.

But lead author Fangfang Yao, a CIRES visiting fellow, now a climate fellow at University of Virginia, said the news is not entirely bleak. With this new method of tracking lake water storage trends and the reasons behind them, scientists can give water managers and communities insight into how to better protect critical sources of water and important regional ecosystems.

"This is the first comprehensive assessment of trends and drivers of global lake water storage variability based on an array of satellites and models," Yao said.

He was motivated to do the research by the environmental crises in some of Earth's largest water bodies, such as the drying of the Aral Sea between Kazakhstan and Uzbekistan.

So he and colleagues from the University of Colorado Boulder, Kansas State University, France, and Saudi Arabia created a technique to measure changes in water levels in nearly 2,000 of the world's biggest lakes and reservoirs, which represent 95 percent of the total lake water storage on Earth.

The team combined three decades of observations from an array of satellites with models to quantify and attribute trends in lake storage globally.

Globally, freshwater lakes and reservoirs store 87 percent of the planet's water, making them a valuable resource for both human and Earth ecosystems. Unlike rivers, lakes are not well monitored, yet they provide water for a large part of humanity -- even more than rivers.

But despite their value, long-term trends and changes to water levels have been largely unknown -- until now.

"We have pretty good information on iconic lakes like Caspian Sea, Aral Sea and Salton Sea, but if you want to say something on a global scale, you need reliable estimates of lake levels and volume," said Balaji Rajagopalan, a CIRES fellow, professor of engineering at CU Boulder, and co-author. "With this novel method …we are able to provide insights into global lake level changes with a broader perspective."

For the new paper, the team used 250,000 lake-area snapshots captured by satellites between 1992-2020 to survey the area of 1,972 of Earth's biggest lakes. They collected water levels from nine satellite altimeters and used long-term water levels to reduce any uncertainty. For lakes without a long-term level record, they used recent water measurements made by newer instruments on satellites. Combining recent level measurements with longer-term area measurements allowed scientists to reconstruct the volume of lakes dating back decades.

The results were staggering: 53 percent of lakes globally experienced a decline in water storage. The authors compare this loss with the magnitude of 17 Lake Meads, the largest reservoir in the United States.

To explain the trends in natural lakes, the team leveraged recent advancements in water use and climate modeling. Climate change and human water consumption dominated the global net decline in natural lake volume and water losses in about 100 large lakes, Yao said. "And many of the human and climate change footprints on lake water losses were previously unknown, such as the desiccations of Lake Good-e-Zareh in Afghanistan and Lake Mar Chiquita in Argentina."

Lakes in both dry and wet areas of the world are losing volume. The losses in humid tropical lakes and Arctic lakes indicate more widespread drying trends than previously understood.

Yao and his colleagues also assessed storage trends in reservoirs. They found that nearly two-thirds of Earth's large reservoirs experienced significant water losses.

"Sedimentation dominated the global storage decline in existing reservoirs," said Ben Livneh, also a co-author, CIRES fellow, and associate professor of engineering at CU Boulder. In long-established reservoirs -- those that filled before 1992 -- sedimentation was more important than droughts and heavy rainfall years.

While the majority of global lakes are shrinking, 24 percent saw significant increases in water storage. Growing lakes tend to be in underpopulated areas in the inner Tibetan Plateau and Northern Great Plains of North America and in areas with new reservoirs such as the Yangtze, Mekong, and Nile river basins.

The authors estimate roughly one-quarter of the world's population, 2 billion people, resides in the basin of a drying lake, indicating an urgent need to incorporate human consumption, climate change, and sedimentation impacts into sustainable water resources management.

And their research offers insight into possible solutions, Livneh said. "If human consumption is a large factor in lake water storage decline, then we can adapt and explore new policies to reduce large-scale declines."

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