Two-million-year-old DNA has been identified for the first time – opening a ‘game-changing’ new chapter in the history of evolution.
Microscopic fragments of environmental DNA were found in Ice Age sediment in northern Greenland. Using cutting-edge technology, researchers discovered the fragments are one million years older than the previous record for DNA sampled from a Siberian mammoth bone.
The ancient DNA has been used to map a two-million-year-old ecosystem which weathered extreme climate change. Researchers hope the results could help to predict the long-term environmental toll of today’s global warming.
The discovery was made by a team of scientists led by Professor Eske Willerslev and Professor Kurt H. Kjær. Professor Willerslev is a Fellow of St John’s College, University of Cambridge, and Director of the Lundbeck Foundation GeoGenetics Centre at the University of Copenhagen where Professor Kjær, a geology expert, is also based.
The results of the 41 usable samples found hidden in clay and quartz are published today (7 DECEMBER 2022) in Nature.
Professor Willerslev said: “A new chapter spanning one million extra years of history has finally been opened and for the first time we can look directly at the DNA of a past ecosystem that far back in time..
“DNA can degrade quickly but we’ve shown that under the right circumstances, we can now go back further in time than anyone could have dared imagine.”
Professor Kjær said: “The ancient DNA samples were found buried deep in sediment that had built-up over 20,000 years. The sediment was eventually preserved in ice or permafrost and, crucially, not disturbed by humans for two million years.”
The incomplete samples, a few millionths of a millimetre long, were taken from the København Formation, a sediment deposit almost 100 metres thick tucked in the mouth of a fjord in the Arctic Ocean in Greenland’s northernmost point. The climate in Greenland at the time varied between Arctic and temperate and was between 10-17C warmer than Greenland is today. The sediment built up metre by metre in a shallow bay.
Scientists discovered evidence of animals, plants and microorganisms including reindeer, hares, lemmings, birch and poplar trees. Researchers even found that Mastodon, an Ice Age mammal, roamed as far as Greenland before later becoming extinct. Previously it was thought the range of the elephant-like animals did not extend as far as Greenland from its known origins of North and Central America.
Detective work by 40 researchers from Denmark, the UK, France, Sweden, Norway, the USA and Germany, unlocked the secrets of the fragments of DNA. The process was painstaking – first they needed to establish whether there was DNA hidden in the clay and quartz, and if there was, could they successfully detach the DNA from the sediment to examine it? The answer, eventually, was yes. The researchers compared every single DNA fragment with extensive libraries of DNA collected from present-day animals, plants and microorganisms. A picture began to emerge of the DNA from trees, bushes, birds, animals and microorganisms.
Some of the DNA fragments were easy to classify as predecessors to present-day species, others could only be linked at genus level, and some originated from species impossible to place in the DNA libraries of animals, plants and microorganisms still living in the 21st century.
The two-million-year-old samples also help academics build a picture of a previously unknown stage in the evolution of the DNA of a range of species still in existence today.
Professor Kjær said: “Expeditions are expensive and many of the samples were taken back in 2006 when the team were in Greenland for another project, they have been stored ever since.
“It wasn’t until a new generation of DNA extraction and sequencing equipment was developed that we’ve been able to locate and identify extremely small and damaged fragments of DNA in the sediment samples. It meant we were finally able to map a two-million-year-old ecosystem.”
Assistant Professor Mikkel W. Pedersen, co-first author on the paper and also based at the Lundbeck Foundation GeoGenetics Centre, said: “The Kap København ecosystem, which has no present-day equivalent, existed at considerably higher temperatures than we have today – and because, on the face of it, the climate seems to have been similar to the climate we expect on our planet in the future due to global warming.
“One of the key factors here is to what degree species will be able to adapt to the change in conditions arising from a significant increase in temperature. The data suggests that more species can evolve and adapt to wildly varying temperatures than previously thought. But, crucially, these results show they need time to do this. The speed of today’s global warming means organisms and species do not have that time so the climate emergency remains a huge threat to biodiversity and the world – extinction is on the horizon for some species including plants and trees.”
While reviewing the ancient DNA from the Kap København Formation, the researchers also found DNA from a wide range of microorganisms, including bacteria and fungi, which they are continuing to map. A detailed description of how the interaction – between animals, plants and single-cell organisms – within the former ecosystem at Greenland’s northernmost point worked biologically will be presented in a future research paper.
It is now hoped that some of the ‘tricks’ of the two-million-year-old plant DNA discovered may be used to help make some endangered species more resistant to a warming climate.
Professor Kjær said: “It is possible that genetic engineering could mimic the strategy developed by plants and trees two million years ago to survive in a climate characterised by rising temperatures and prevent the extinction of some species, plants and trees. This is one of the reasons this scientific advance is so significant because it could reveal how to attempt to counteract the devastating impact of global warming.”
The findings from the Kap København Formation in Greenland have opened up a whole new period in DNA detection.
Professor Willerslev explained: “DNA generally survives best in cold, dry conditions such as those that prevailed during most of the period since the material was deposited at Kap København. Now that we have successfully extracted ancient DNA from clay and quartz, it may be possible that clay may have preserved ancient DNA in warm, humid environments in sites found in Africa.
“If we can begin to explore ancient DNA in clay grains from Africa, we may be able to gather ground-breaking information about the origin of many different species – perhaps even new knowledge about the first humans and their ancestors – the possibilities are endless.”
Rare ‘big fuzzy green ball’ comet visible in B.C. skies, a 50000-year sight
In the night sky, a comet is flying by Earth for the first time in 50,000 years.
Steve Coleopy, of the South Cariboo Astronomy Club, is offering some tips on how to see it before it disappears.
The green-coloured comet, named C/2022 E3 (ZTF), is not readily visible to the naked eye, although someone with good eyesight in really dark skies might be able to see it, he said. The only problem is it’s getting less visible by the day.
“Right now the comet is the closest to earth and is travelling rapidly away,” Coleopy said, noting it is easily seen through binoculars and small telescopes. “I have not been very successful in taking a picture of it yet, because it’s so faint, but will keep trying, weather permitting.”
At the moment, the comet is located between the bowl of the Big Dipper and the North Star but will be moving toward the Planet Mars – a steady orange-coloured point of light- in the night sky over the next couple of weeks, according to Coleopy.
“I have found it best to view the comet after 3:30 in the morning, after the moon sets,” he said. “It is still visible in binoculars even with the moon still up, but the view is more washed out because of the moonlight.”
He noted the comet looks like a “big fuzzy green ball,” as opposed to the bright pinpoint light of the stars.
“There’s not much of a tail, but if you can look through the binoculars for a short period of time, enough for your eyes to acclimatize to the image, it’s quite spectacular.”
To know its more precise location on a particular evening, an internet search will produce drawings and pictures of the comet with dates of where and when the comet will be in each daily location.
Coleopy notes the comet will only be visible for a few more weeks, and then it won’t return for about 50,000 years.
Extreme species deficit of nitrogen-converting microbes in European lakes
Sampling of Lake Constance water from 85 m depth, in which ammonia-oxidizing archaea make up as much as 40% of all microorganisms
An international team of researchers led by microbiologists from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH in Braunschweig, Germany, shows that in the depths of European lakes, the detoxification of ammonium is ensured by an extremely low biodiversity of archaea. The researchers recently published their findings in the prestigious international journal Science Advances. The team led by environmental microbiologists from the Leibniz Institute DSMZ has now shown that the species diversity of these archaea in lakes around the world ranges from 1 to 15 species. This is of particularly concern in the context of global biodiversity loss and the UN Biodiversity Conference held in Montreal, Canada, in December 2022. Lakes play an important role in providing freshwater for drinking, inland fisheries, and recreation. These ecosystem services would be at danger from ammonium enrichment. Ammonium is an essential component of agricultural fertilizers and contributes to its remarkable increase in environmental concentrations and the overall im-balance of the global nitrogen cycle. Nutrient-poor lakes with large water masses (such as Lake Constance and many other pre-alpine lakes) harbor enormously large populations of archaea, a unique class of microorganisms. In sediments and other low-oxygen environments, these archaea convert ammonium to nitrate, which is then converted to inert dinitrogen gas, an essential component of the air. In this way, they contribute to the detoxification of ammonium in the aquatic environment. In fact, the species predominant in European lakes is even clonal and shows low genetic microdiversity between different lakes. This low species diversity contrasts with marine ecosystems where this group of microorganisms predominates with much greater species richness, making the stability of ecosystem function provided by these nitrogen-converting archaea potentially vulnerable to environmental change.
Maintenance of drinking water quality
Although there is a lot of water on our planet, only 2.5% of it is fresh water. Since much of this fresh water is stored in glaciers and polar ice caps, only about 80% of it is even accessible to us humans. About 36% of drinking water in the European Union is obtained from surface waters. It is therefore crucial to understand how environmental processes such as microbial nitrification maintain this ecosystem service. The rate-determining phase of nitrification is the oxidation of ammonia, which prevents the accumulation of ammonium and converts it to nitrate via nitrite. In this way, ammonium is prevented from contaminating water sources and is necessary for its final conversion to the harmless dinitrogen gas. In this study, deep lakes on five different continents were investigated to assess the richness and evolutionary history of ammonia-oxidizing archaea. Organisms from marine habitats have traditionally colonized freshwater ecosystems. However, these archaea have had to make significant changes in their cell composition, possible only a few times during evolution, when they moved from marine habitats to freshwaters with much lower salt concentrations. The researchers identified this selection pressure as the major barrier to greater diversity of ammonia-oxidizing archaea colonizing freshwaters. The researchers were also able to determine when the few freshwater archaea first appeared. Ac-cording to the study, the dominant archaeal species in European lakes emerged only about 13 million years ago, which is quite consistent with the evolutionary history of the European lakes studied.
Slowed evolution of freshwater archaea
The major freshwater species in Europe changed relatively little over the 13 million years and spread almost clonally across Europe and Asia, which puzzled the researchers. Currently, there are not many examples of such an evolutionary break over such long time periods and over large intercontinental ranges. The authors suggest that the main factor slowing the rapid growth rates and associated evolutionary changes is the low temperatures (4 °C) at the bottom of the lakes studied. As a result, these archaea are restricted to a state of low genetic diversity. It is unclear how the extremely species-poor and evolutionarily static freshwater archaea will respond to changes induced by global climate warming and eutrophication of nearby agricultur-al lands, as the effects of climate change are more pronounced in freshwater than in marine habitats, which is associated with a loss of biodiversity.
Publication: Ngugi DK, Salcher MM, Andre A-S, Ghai R., Klotz F, Chiriac M-C, Ionescu D, Büsing P, Grossart H-S, Xing P, Priscu JC, Alymkulov S, Pester M. 2022. Postglacial adaptations enabled coloniza-tion and quasi-clonal dispersal of ammonia oxidizing archaea in modern European large lakes. Science Advances: https://www.science.org/doi/10.1126/sciadv.adc9392
PhDr. Sven-David Müller, Head of Public Relations, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH
Phone: ++49 (0)531/2616-300
About the Leibniz Institute DSMZ
The Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures is the world’s most diverse collection of biological resources (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). Microorganisms and cell cultures are collected, investigated and archived at the DSMZ. As an institution of the Leibniz Association, the DSMZ with its extensive scientific services and biological resources has been a global partner for research, science and industry since 1969. The DSMZ was the first registered collection in Europe (Regulation (EU) No. 511/2014) and is certified according to the quality standard ISO 9001:2015. As a patent depository, it offers the only possibility in Germany to deposit biological material in accordance with the requirements of the Budapest Treaty. In addition to scientific services, research is the second pillar of the DSMZ. The institute, located on the Science Campus Braunschweig-Süd, accommodates more than 82,000 cultures and biomaterials and has around 200 employees. www.dsmz.de
Scientists are closing in on why the universe exists
Particle astrophysicist Benjamin Tam hopes his work will help us understand a question. A very big one.
“The big question that we are trying to answer with this research is how the universe was formed,” said Tam, who is finishing his PhD at Queen’s University.
“What is the origin of the universe?”
And to answer that question, he and dozens of fellow scientists and engineers are conducting a multi-million dollar experiment two kilometres below the surface of the Canadian Shield in a repurposed mine near Sudbury, Ontario.
The Sudbury Neutrino Observatory (SNOLAB) is already famous for an earlier experiment that revealed how neutrinos ‘oscillate’ between different versions of themselves as they travel here from the sun.
This finding proved a vital point: the mass of a neutrino cannot be zero. The experiment’s lead scientist, Arthur McDonald, shared the Nobel Prize in 2015 for this discovery.
The neutrino is commonly known as the ‘ghost particle.’ Trillions upon trillions of them emanate from the sun every second. To humans, they are imperceptible except through highly specialized detection technology that alerts us to their presence.
Neutrinos were first hypothesized in the early 20th century to explain why certain important physics equations consistently produced what looked like the wrong answers. In 1956, they were proven to exist.
Tam and his fellow researchers are now homing in on the biggest remaining mystery about these tiny particles.
Nobody knows what happens when two neutrinos collide. If it can be shown that they sometimes zap each other out of existence, scientists could conclude that a neutrino acts as its own ‘antiparticle’.
Such a conclusion would explain how an imbalance arose between matter and anti-matter, thus clarifying the current existence of all the matter in the universe.
It would also offer some relief to those hoping to describe the physical world using a model that does not imply none of us should be here.
Guests in this episode (in order of appearance):
Benjamin Tam is a PhD student in Particle Astrophysics at Queen’s University.
Eve Vavagiakis is a National Science Foundation Astronomy and Astrophysics Postdoctoral Fellow in the Physics Department at Cornell University. She’s the author of a children’s book, I’m A Neutrino: Tiny Particles in a Big Universe.
Erica Caden is a research scientist at SNOLAB. Among her duties she is the detector manager for SNO+, responsible for keeping things running day to day.
*This episode was produced by Nicola Luksic and Tom Howell. It is part of an on-going series, IDEAS from the Trenches, some stories are below.
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