DNA sequencing from soil heralded as ‘moon landing of genomics’

21 Apr 2021

Prof Mikkel Winther Pedersen sampling cave sediments in Mexico. Image: Devlin A Gandy

Researchers have sequenced ancient bear DNA from sediment in a Mexican cave, opening up a ‘new frontier‘ for genomics.

Scientists have made a major breakthrough in DNA sequencing that they have described as “the moon landing of genomics”.

Researchers at the Lundbeck Foundation GeoGenetics Centre at the University of Copenhagen sequenced ancient DNA from soil for the first time. They claim that this could transform how research is carried out in the field because scientists may no longer have to rely on fossils to determine genetic ancestry.

Led by the foundation’s director and fellow at the University of Cambridge, Prof Eske Willerslev, the team used microscopic fragments of DNA found in Chiquihuite Cave in Mexico to recreate the genomes of ancient animals, plants and bacteria. Among them was an ancestor of North America’s most common bear, the black bear.

‘Analysis of DNA found in soil could have the potential to expand the narrative about everything from the evolution of species to developments in climate change’

Chiquihuite Cave is a high-altitude site located 2,750 metres above sea level, where nearly 2,000 stone tools have been discovered.

The study, published in Current Biology, is said to be the first to sequence environmental DNA from soil and sediment. Samples were composed of faeces and urine droplets from the ancient bear, which allowed scientists to recreate the genomes of two species: the Stone Age American black bear and a short-faced bear called Arctodus simus, which went extinct 12,000 years ago.

Arctodus simus was a huge predatory bear that stood at nearly two metres tall on all fours and could weigh up to 1,000kg.

“When an animal or a human urinates or defecates, cells from the organism are also excreted. And the DNA fragments from these cells are what we can detect in the soil samples,” Willerslev explained.

“Using extremely powerful sequencing techniques, we reconstructed genomes – genetic profiles – based on these fragments for the first time. We have shown that hair, urine and faeces all provide genetic material which, in the right conditions, can survive for much longer than 10,000 years.

“All over the world, everyone scientifically involved in the study of ancient DNA recognised the need to reconstruct genomes from fragments found in soil or sediment. Being able to do that for the first time means we have opened up a new frontier.

“Analysis of DNA found in soil could have the potential to expand the narrative about everything from the evolution of species to developments in climate change – this is the moon landing of genomics because fossils will no longer be needed.”

The paper’s first author, Prof Mikkel Winther Pedersen, added: “We have published for the first time a DNA profile of an American black bear that lived in a mountain cave in northern Mexico in the Stone Age. I’m not exaggerating when I say that the potential to extract this type of information from a soil sample of a mere few grams will revolutionise our field.”

Lisa Ardill was careers editor at Silicon Republic until June 2021