Author: Noemí Alonso
We have already seen how ancient DNA can help us tackle the effects of climate change, for example by inspiring new solutions to improve crops resilience through their interaction with soil microorganisms. But how can we do that? how do we “read” an ancient gene?
Imagine finding a jigsaw puzzle with thousands of pieces, broken, incomplete, and without the picture on the box. To make things harder, someone has also mixed pieces that don’t belong to the original puzzle. This is the starting point when working with DNA extracted from frozen Arctic soils.
In the TOLERATE project, researchers are looking for molecular traces: fragments of DNA from microorganisms that lived thousands of years ago, under very different climates, and often more extreme, than those we see today. These microorganisms were part of ancient soil and rhizosphere communities, closely associated with plant roots. You can obtain more information about the relationship between plant rhizosphere and crop resilience in our post How the TOLERATE Project Supports Agriculture in a Changing Climate but, how do scientists read these ancient genes? Keep reading to find out.
Finding the puzzle pieces in permafrost
When a microorganism dies, its DNA begins to break down and usually disappears quite quickly. But in permanently frozen soils, known as permafrost, the cold acts like a time capsule. DNA can survive for thousands of years. Still, after so much time, it reaches us chemically damaged, broken into tiny fragments, and mixed with DNA from countless different species.
One of the most critical steps is extracting these samples without contaminating them with modern DNA. To do this, researchers work in specialized laboratories with constant controls to detect contamination. They wear protective clothing and use sterilized tools, because even a single modern cell can introduce DNA and completely distort the interpretation of the data.
Reading piece by piece, without the full picture
When scientists sequence ancient DNA, they don’t get long, complete genes. Instead, they obtain millions of very short sequences, sometimes only 30, 50, or 70 DNA “letters” long. Each of these fragments is like a half sentence from a book written thousands of years ago, in a language that is no longer spoken in quite the same way.
This is where bioinformatics comes in. Thanks to powerful computer tools, scientists can search for fragments that fit together, detect overlaps, and group pieces that likely belong to the same organism. Doing this manually would be practically impossible.
Even if it’s not always possible to rebuild a complete genome, researchers can still recover fragments of genes, partial metabolic pathways, and families of genes with interesting functions. It’s like recreating the original image while knowing that some pieces are forever lost.
Spotting the “wrinkles” of ancient DNA
One of the most important challenges when studying ancient DNA is making sure it really is ancient, and not the result of modern contamination. To confirm this, scientists look for what you might call the “chemical wrinkles” of DNA, the marks that time leaves behind.
These include:
- Chemical changes in DNA bases: Over time, some DNA bases undergo slow chemical modifications, such as losing functional groups. These changes are extremely difficult to reproduce artificially.
- Damage patterns at fragment ends: Ancient DNA breaks in characteristic ways. The chemical damage at the ends of fragments follows recognizable, non-random patterns that act like a fingerprint.
- Typical fragment length distributions: As DNA ages, it breaks into fragments of characteristic lengths. Experts can recognize these patterns in the overall mix of fragments.
By evaluating these signals, researchers can’t usually determine the exact age of a sample, but they can confirm whether it has been preserved. If these signals are missing, modern contamination is suspected, for example, DNA from a researcher or from the surrounding environment, and this is relatively easy to detect.
Turning ancient genes into new ideas
Once ancient DNA fragments have been identified, they can tell us how past organisms lived and which genes helped them survive extreme conditions. But how do we extract useful information from them?
- Comparing ancient and modern genes: By aligning ancient genes with those of modern microorganisms, scientists can see which genes have changed over time and which have remained stable. This helps identify which genes are essential and which are not.
- Inferring gene function: Even if a gene no longer exists today, its function can often be inferred from its sequence. For example, those that are similarity to known genes that’s involved the production of protective biomolecules.
- Detecting adaptations to past extreme climates: Researchers have found genes linked to enhanced DNA repair or encode proteins that remain stable in extreme cold or heat, suggesting adaptation to high radiation environments and rapid responses to abrupt temperature changes.
By combining all this information, scientists can gradually reconstruct ancient soil and rhizosphere ecosystems: which organisms lived in association with plants roots, under what environmental conditions, and how they responded to climatic change.
In this sense, ancient DNA samples are an ecological and evolutionary record, showing us how life found innovative solutions to extreme environments. This is exactly the kind of knowledge the TOLERATE project aims to turn into practical applications, such as:
- Identifying stress-resistance genes that help tolerate drought, cold, or high salinity.
- Discovering microbial functions that support plant resilience through root-associated bacteria and reduce the need for chemical treatments.
- Learning how to adapt to climate change by understanding how life survived major environmental changes in the past.
From frozen soils to future solutions
In conclusion, ancient DNA metagenomics doesn’t give us complete answers, it offers small fragments of evolutionary history. But sometimes, a few pieces from the past are enough to reveal the bigger picture and provide valuable insights for the future. TOLERATE project builds a directly approach to identify genes involved in stress tolerance, such as those responsible for producing humidifying polysaccharides or biosurfactant betaines. The aim is development of climate-resilient plant-microbe interactions, the reconstruction of robust enzymes for industrial use, and the engineering of microbial strains for sustainable bioproduction.