The World's Largest Virus Was Just Resurrected From 34,000-Year-Old Permafrost
By Joseph Stromberg
It's not a threat to humans, but does show that ancient viruses
can persist for millennia and remain a potential health threat
By Joseph Stromberg
March 3, 2014
Deep within the Siberian permafrost, nearly 100 feet underneath the frozen ground, it sat dormant, for centuries and centuries. Above ground, the glaciers receded, ancient humans arrived, and eventually, civilization developed.
Now, it's been thawed and revived, thanks to a team of French scientists. It's a virus, and its zombie-like resurrection goes to show that the microbes can persist for far longer than scientists have previously imagined.
For tens of thousands of years, the virus remained entirely frozen. The microbe, however, wasn't quite dead—partly because any virus, by the standards of biology, can't be truly be described as alive <http://www.scientificamerican.com/article/are-viruses-alive-2004/> . All viruses require host cells to reproduce, and in between reproductive cycles, they persist as an inert particle called a virion, roughly analogous to a plant's seed.
In 2000, the scientists, led by Jean-Michel Claverie <http://www.igs.cnrs-mrs.fr/spip.php?article39&lang=fr> and Chantal Abergel <http://www.igs.cnrs-mrs.fr/spip.php?article88&lang=fr> of the Mediterranean Institute of Microbiology, <http://www.igs.cnrs-mrs.fr/?lang=en> arrived in Anyuysk <http://en.wikipedia.org/wiki/Anyuysk> , a remote town in Siberia's Chukotka <http://en.wikipedia.org/wiki/Chukotka_Autonomous_Okrug> region, to search for new viruses in previously unexplored environments. It'd previously been speculated (and has since been proven <http://www.nytimes.com/2012/02/21/science/new-life-from-an-arctic-flower-that-died-32000-years-ago.html> ) that organisms could be frozen for tens of thousands of years and then successfully revived, so the researchers drilled deep into an outcrop of permanently frozen ground along the banks of the Anuy River to search for some.
The Chukotka region, shown in red, where the scientists sampled permafrost. (Image via Wikimedia Commons/Marmelad <http://en.wikipedia.org/wiki/File:Map_of_Russia_-_Chukotka_Autonomous_Okrug_%282008-03%29.svg> )
They handled the core of frozen soil they extracted with extreme care, coating its outer surface with rubbing alcohol to eliminate contamination, then extracting a tiny sample of soil from its center and storing it in a sterile bag. Using radiocarbon dating <http://www.smithsonianmag.com/science-nature/a-new-leap-forward-for-radiocarbon-dating-81047335/> , the scientists dated the soil's age to somewhere between 34,000 and 37,000 years.
Years passed, and the scientists eventually analyzed the sample, along with others. More than a decade later, they've finally announced they've indeed found a viable virus in the sample of permafrost—and it's much more unusual than they'd expected.
"We guessed that virions could remain infectious at least that long," Claverie says. "The surprise came more from the fact that it was a giant virus and of a type totally different from the previous [modern] ones."
Until 2003, it was thought that all viruses were tiny—completely invisible under a standard light microscope <http://en.wikipedia.org/wiki/Optical_microscope> and a fraction of the size of most bacterial cells. Since, several giant viruses have been discovered <http://www.sciencemag.org/content/299/5615/2033> , including pandoraviruses, discovered by Claverie and Abergel <http://www.nature.com/news/giant-viruses-open-pandora-s-box-1.13410> in a water sample collected off the coast of Chile, which held the size record with a length of about one micrometer <http://en.wikipedia.org/wiki/Micrometre> , or one-thousandth of a millimeter.
But their new virus Pithovirus sibericum, described in a paper published today in Proceedings of the National Academy of Sciences <http://www.pnas.org/cgi/doi/10.1073/pnas.1320670111> , is an astonishing 1.5 micrometers long, between 10 and 100 times as large as the average-sized virus. Under a microscope, it's easily visible as an oval rimmed by a dark black envelope <http://en.wikipedia.org/wiki/Viral_envelope> with a perforated plug at the end, about the size of a bacterial cell.
Detailed microscope views of the virus: A focuses on its perforated plug; B shows a cross-section, with the arrow pointing to a tubular structure at the center; C shows a top view of the plug; D shows a bottom view of the virus' opposite end. (Image courtesy of Julia Bartoli and Chantal Abergel, IGS and CNRS-AMU)
It poses no danger to humans, because it exclusively infects single-celled organisms called amoebae <http://en.wikipedia.org/wiki/Amoeba> —something the scientists discovered when they revived the microbe from its inert virion form by warming it up and putting it in a petri dish with live amoebae. Once revived, the virus entered the amoebae cells, hijacked the cells' metabolic machinery to create many copies of itself, and split the cells open, killing them and freeing itself to infect further cells.
Previously-known giant viruses also infect amoebae, likely because of how easy it is to enter them. Amoebae feed through phagocytosis <http://en.wikipedia.org/wiki/Phagocytosis> , using their cellular membranes to engulf particles and organisms; for a giant virus to get inside an amoeba, all it has to do it let itself be engulfed. Because most human and other animals cells don't engulf particles in this way, viruses that infect us generally have to use more complex entry methods, which prohibit such an enormous size.
For the scientists, the most significant aspect of the new discovery is what they found when they isolated the virus' DNA and sequenced its genes. "Its genome size is much smaller than expected from the particle size, only 500 genes," Claverie says, "where the other two families of giant viruses have more than a thousand." Additionally, the new virus's replication process is much more similar to that of standard-size virus, rather than the other giant viruses, leading Claverie to describe it as something of a "bridge" between the giant viruses and the traditional ones.
Until now, the two families of giant virus discovered (megaviruses <http://en.wikipedia.org/wiki/Megavirus_chilensis> and pandoraviruses <http://en.wikipedia.org/wiki/Pandoravirus> ) were very genetically similar. The discovery of a radically different giant virus in a randomly-selected sample of permafrost, the researchers say, indicates that giant viruses are much more common and more diverse than was previously thought.
There's also the fact that this virus survived for at least 30,000 years in frozen soil. Because viruses don't engage in most of the self-sustaining activities performed by all forms of life (they don't harness energy to regulating their own metabolism, for instance), it seems likely that they can survive in an inert state far longer than any life form. If the only limit is the amount of time their DNA can persist, it's possible they can survive several million years before it's irreparably damaged by natural radioactivity from the Earth. Claverie and Abergel are currently sampling older layers of frozen soil to search for even more ancient viruses.
But even though this particular virus poses no human health threat, its discovery raises unsettling questions. "[This] is a good demonstration that the notion that a virus could be 'eradicated' from the planet is plain wrong, and give us a false sense of security," Claverie says. As the Arctic and subarctic warm, "mining and drilling mean bringing human settlements and digging through these ancient layers for the first time in millions of years. If viable virions are still there, this is a good recipe for disaster."
Joseph Stromberg writes about science, technology and the environment for Smithsonian and has also contributed to Slate, the Verge, Salon and other outlets. <https://plus.google.com/+JosephStromberg/?rel=author>
Plants Frozen
Under a Glacier
for 400 Years
Can Come Back
to Life
Long-buried mosses recently exposed in the wake
of a Canadian glacier's retreat are sprouting new growth, a study shows
By Joseph Stromberg
smithsonianmag.com
May 27, 2013
From 1550 to 1580, the period of cooling known as the Little Ice Age <http://en.wikipedia.org/wiki/Little_Ice_Age> hit Ellesmere Island <http://en.wikipedia.org/wiki/Ellesmere_Island> , in extreme northern Nunavut, Canada. As temperatures plunged, most of the island was swallowed by the advance of glaciers. The vegetation that had blanketed the terrain—mostly mosses and lichens—was buried under dozens of feet of ice.
In recent years, the reverse has happened. As a result of climate change, glaciers around the world have retreated rapidly, and Ellesmere Island has been no exception. The island’s Teardrop Glacier has retreated more than 650 feet, revealing numerous clumps of blackened, seemingly dead vegetation such as mosses and lichens that had been frozen for centuries.
But some of the vegetation was in fact far from dead. A research team from the University of Alberta led by Catherine La Farge <http://www.biology.ualberta.ca/faculty/catherine_lafarge/> surveyed the area revealed by the retreat of Teardrop Glacier and noticed that some of the largely blackened plants, including several mosses, had small green stems and lateral branches growing from them, indicating that they were experiencing recent growth.
The team showed that these plants, found right next to the edge of the retreating glacier, belonged to different species than those growing on the surrounding terrain, indicating they’d truly been buried until recently. Radiocarbon dating of the blackened parts of the plants confirmed that they were between 400 and 615 years old. The findings were published today in the Proceedings of the National Academy of Sciences <http://www.pnas.org/cgi/doi/10.1073/pnas.1304199110>.
Click for image: <http://blogs.smithsonianmag.com/science/files/2013/05/13-04199large2.jpg>
Discolored mosses and lichens revealed by the melting of Teardrop Glacier. Image courtesy of Catherine La Farge
The researchers took samples from some of the plants just next to the glacier, which they determined had been uncovered sometime in the past few years, along with some that were still partially encased in ice. Back in the lab, they closely examined the samples and noted that new growth—green stems and shoots—was occurring on the centuries-old plants.
Click for image: <http://blogs.smithsonianmag.com/science/files/2013/05/new-growth.jpg>
A new shoot grows on a centuries-old sample of Bartramia ithyphylla. LIA refers to “Little Ice Age” growth, which occurred more than 400 years ago. Image via PNAS/La Farge et. al.
Additionally, they ground up 24 different samples and sprinkled them over nutrient-enriched soil. Within months, plants had sprouted in 11 different petri dishes, representing seven of the different plants sampled.
Click for image: <http://blogs.smithsonianmag.com/science/files/2013/05/comparison.jpg>
Three different types of resurrected plants grow intermixed in a petri dish,
next to a detail of a new shoot. Image via PNAS/La Farge et. al.
This remarkable resurrection was enabled by the fact that the plants were preserved at sub-freezing temperatures, allowing at least some of their cells to survive. Further, they all belong to a group of plants (called bryophytes <http://en.wikipedia.org/wiki/Bryophyte> ) that grow clonally, so each of their cells can reproduce and then differentiate into any sort of cell that makes up the organism (a quality called totipotency <http://en.wikipedia.org/wiki/Totipotency#Totipotency> ). Additionally, microscopic analysis of the cells of the blackened, seemingly dead plants showed that their structural integrity had been well preserved by the ice, which in some cases left cell organelles and other tiny structures intact.
The discovery could substantially change our understanding of the way ecosystems regenerate after glacial retreat—a pretty important topic, given what’s currently happening to wide swaths of the Arctic given current melting trends <http://blogs.smithsonianmag.com/science/2013/03/the-greening-of-the-arctic-is-underway/> . If glaciers serve as reservoirs of plant species that can potentially regenerate, it means that the ecosystems that sprout in the glaciers’ wake are more likely to be made up of these original plant types rather than the quickly-growing, newly arrived colonizing species scientists had previously assumed would dominate such environments.
Although most of the ecological news brought to us by climate change has been uniformly depressing, these newly resurrected plants, which now join a host of other life capable of regrowth after dormancy <http://blogs.smithsonianmag.com/science/2013/03/sea-monkeys-ferns-and-frozen-frogs-natures-very-own-resurrecting-organisms/> , show how incredibly durable and resilient life can be.
The Remnants of Prehistoric
Plant Pollen Reveal
that Humans
Shaped Forests
11,000 Years Ago
The discoveries could boost indigenous populations' claims
to ancestral lands long thought to be untouched by human activity
ByJosie Garthwaite
smithsonianmag.com
March 5, 2014
A tropical forest writes much of its history at large scale, producing trees as tall as skyscrapers and flowers the size of carry-on luggage. But by zooming in, scientists are uncovering chapters in forest history that were influenced by human activity far earlier than anyone thought.
A new study of pollen samples extracted from tropical forests in southeast Asia suggests humans have shaped these landscapes for thousands of years. Although scientists previously believed the forests were virtually untouched by people, researchers are now pointing to signs of imported seeds, plants cultivated for food, and land clearing as early as 11,000 years ago—around the end of the last Ice Age <http://www.epa.gov/gmpo/edresources/pleistocene.html> .
The study <http://www.sciencedaily.com/releases/2014/01/140124082608.htm> , to be published in the peer-reviewed Journal of Archaeological Science <http://www.sciencedirect.com/science/article/pii/S030544031300441X> comes from researchers led by paleoecologist Chris Hunt, of Queen’s University, Belfast, who analyzed existing data and examined samples from Borneo, Sumatra, Java, Thailand and Vietnam.
Pollen offers an important key for unlocking the history of human activity in a region where dense tropical forests make traditional excavations slow, arduous work, and thick canopies hinder aerial surveys. Reliance on building materials that perish with the centuries (rather than stone or ceramic) can make it difficult to recognize signs of long-gone inhabitants. Pollen, however, can survive for thousands of years in the right conditions and paint a picture of vegetation over time.
In the Kelabit Highlands of Borneo, for example, pollen samples dated to about 6,500 years ago contain abundant charcoal evidence of fire. That alone doesn’t reveal a human hand. But scientists know that specific weeds and trees that flourish in charred ground would typically emerge in the wake of naturally occurring or accidental blazes. What Hunt’s team found instead was evidence of fruit trees. "This indicates that the people who inhabited the land intentionally cleared it of forest vegetation and planted sources of food in its place,” Hunt explained in a statement <http://www.sciencedaily.com/releases/2014/01/140124082608.htm> about the study.
Hunt’s team also looked at the types of pollen reported in cores extracted from very isolated areas where, in all likelihood, humans did not intervene with the succession of plants that would have come about simply because of changes in temperature, rainfall, and competition among species. The patterns in these cores could then be used as a proxy for what to expect without human intervention. When layers sampled from other, comparable sites in the region failed match up, it raised a flag for the researchers that humans may have disrupted the natural succession through burning, cultivation, or other activities.
"Ever since people had the ability to make stone tools and control fire, they were able to manipulate the environment," explained biologist David Lentz, who directs the Center for Field Studies at the University of Cincinnati. "In pre-agricultural times, they would burn forest to improve hunting and increase the growth of plants that were edible—often weedy plants with lots of seeds. This is a pattern that we see all over the world." It’s not surprising, he added, to see it documented in Southeast Asia.
And yet, Hunt said, "It has long been believed that the rainforests of the Far East were virgin wildernesses, where human impact has been minimal.” To the contrary, his team traced signs of vegetation changes resulting from human actions. “While it could be tempting to blame these disturbances on climate change,” he said, “that is not the case as they do not coincide with any known periods of climate change.
This kind of research is about more than glimpsing ancient ways of life. It could also present powerful information for people who live in these forests today. According to Hunt, “Laws in several countries in Southeast Asia do not recognize the rights of indigenous forest dwellers on the grounds that they are nomads who leave no permanent mark on the landscape.” The long history of forest management traced by this study, he says, offers these groups “a new argument in their case against eviction.”
Such tensions have played out beyond Southeast Asia. In Australia, for example, “the impact of humans on the environment is clear stretching back over 40,000 years or so,” says environmental geoscientist Dan Penny, of The University of Sydney. And yet, he says, “the material evidence of human occupation is scarce.” Starting in the 18th century, the British used that fact "to justify their territorial claim" to land inhabited by Aboriginal Australians—declaring it terra nullius (belonging to no-one), establishing a colony, and eventually claiming sovereignty over the entire continent.
This latest study comes as part of a larger discussion about when and how our species began shaping the world around us. “Humans and pre-humans have been present in Asia for a very long time, and there have been a number of studies that point to a very long history of human alteration of the natural environment,” says Penny. Hunt’s work in Southeast Asia, he says, makes a “valuable contribution” to that discussion, and to a broader debate surrounding the timing of what scientists call the Anthropocene <http://www.smithsonianmag.com/science-nature/what-is-the-anthropocene-and-are-we-in-it-164801414/> —a proposed period in human history when activity began to alter natural processes in a significant way.”