TSU specialists in environmental DNA are restoring Siberia's past

Tomsk State University biologists are researching the past of Western Siberia using DNA metabarcoding—a modern-day genetics technology that, compared to the regular micropaleontological approaches, is significantly more efficient in studying the Earth’s biodiversity. Environmental DNA can help understand the processes behind the climatic transformations in the macroregion and predict future changes. The data on genetic variability of vegetation and microorganisms of the past can potentially be used for creating new biotechnologies.

“With metabarcoding we can simultaneously identify several taxa in one sample,” explains Natalia Rudaya, head of the project, TSU Biological Institute staff member, and head of the PaleoData laboratory, Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences. “We can acquire information on various organisms’ sedimentary DNA hidden in paleoarchives: To access them, we have to study lake, marine, and terrestrial sediments.”

As part of the project initiated by TSU Biological Institute, scientists completed the study of samples gathered in the Altai Republic’s Lake Balyktukel. Radiocarbon dating of lake sediment extracted using a 2.5-meter core sample enabled the scientists to determine the sediment’s age—7000 years. By analyzing the sedimentary DNA, the team members discovered 118 land plant taxa and 19 aquatic plant taxa.

Lake Balyktukel

Metabarcoding opens a wide array of possibilities for doing taxonomic analysis and restoring the framework of the past’s flora and fauna. The palinological method (study of pollen dust), for one, can provide a lot of data on specific types of vegetation, but fails to do so when it comes to other types.

“This concerns larches, which outline the border between the forests of the Altai mountains and Western Siberia,” shares Natalia Rudaya. Sediments don’t preserve the pollen of larch trees well, meaning that the palinological method is not applicable here. Yet this tree’s data is of utmost importance for us, because it is very sensitive to the slightest changes in the climate and therefore can enable us to track those changes. When it gets warm, larches migrate to the north; by monitoring their movements we can determine the periods of temperature rises and drops.”

The analysis of DNA samples gathered in the Altai Republic showed that the warmest period, during which the sediments were being formed, took place 4000-7000 years ago. It is exactly at that time period when the vegetation was the most diverse. This period coincides with the Holocene optimum. Since then the diversity will have decreased, but during the last few decades there has been a slight increase, which, along with other factors, indicates that the climate is getting warmer.

Extraction of samples at Lake Balyktukel 

Apart from the new data obtained, what makes the project remarkable is that the sedimentary DNA metabarcoding technology was developed in the TSU Biological Institute. Currently, the institute is the only platform in Russia to possess such technology.

Analysis of sedimentary DNA from core samples obtained through dating makes it possible to determine the timeframe for taxon extinction and invasion of non-native species. If the project will be renewed under the program Priority 2030, TSU scientists will get a chance at studying other areas of Western Siberia, among which are the areas with thawing permafrost. By continuing their research, the team will acquire new fundamental data that potentially can be applied In multiple ways.

“Data obtained all around the world via sedimentary DNA analysis is compiled into extensive international databases. It is a unique paleogenetic resource that can be applied in engineering biology,” says Gleb Artyomov, head of the Department of Genetics and Cellular Biology, TSU Biological Institute. “The DNA of the past’s vegetation and microorganisms contain examples of variability that the modern-day flora and fauna simply do not have. The DNA responsible for coding useful proteins and ferments, for instance, can be used in agriculture, microbiology, and genetic engineering.”

Photo provided by Natalya Rudaya