'Time-traveling' pathogens in melting permafrost pose likely risk to environment

Ancient pathogens that escape from melting permafrost have real potential to damage microbial communities and might potentially threaten human health, according to a new study by Giovanni Strona of the European Commission Joint Research Centre and colleagues, published July 27 in the open-access journal PLOS Computational Biology.

The idea that "time-traveling" pathogens trapped in ice or hidden in remote laboratory facilities could break free to cause catastrophic outbreaks has inspired generations of novelists and screenwriters. While melting glaciers and permafrost are giving many types of dormant microbes the opportunity to re-emerge, the potential threats to human health and the environment posed by these microbes have been difficult to estimate.

In a new study, Strona's team quantified the ecological risks posed by these microbes using computer simulations. The researchers performed artificial evolution experiments where digital virus-like pathogens from the past invade communities of bacteria-like hosts. They compared the effects of invading pathogens on the diversity of host bacteria to diversity in control communities where no invasion occurred.

The team found that in their simulations, the ancient invading pathogens could often survive and evolve in the modern community, and about 3 percent became dominant. While most of the dominant invaders had little effect on the composition of the larger community, about 1 percent of the invaders yielded unpredictable results. Some caused up to one third of the host species to die out, while others increased diversity by up to 12 percent compared to the control simulations.

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Genome analysis of 46,000-year-old roundworm from Siberian permafrost reveals novel species

Some organisms, such as tardigrades, rotifers, and nematodes, can survive harsh conditions by entering a dormant state known as "cryptobiosis." In 2018, researchers from the Institute of Physicochemical and Biological Problems in Soil Science RAS in Russia found two roundworms (nematode) species in the Siberian Permafrost. Radiocarbon dating indicated that the nematode individuals have remained in cryptobiosis since the late Pleistocene, about 46,000 years ago. Researchers from the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, the Center for Systems Biology Dresden (CSBD), and the Institute of Zoology at the University of Cologne, all located in Germany, used genome sequencing, assembly, and phylogenetic analysis and found that the permafrost nematode belongs to a previously undescribed species, Panagrolaimus kolymaensis. They showed that the biochemical mechanisms employed by Panagrolaimus kolymaensis to survive desiccation and freezing under laboratory conditions are similar to those of a life-cycle stage in the important biological model Caenorhabditis elegans.

When Anastasia Shatilovich at the Institute of Physicochemical and Biological Problems in Soil Science RAS in Russia revived two frozen individual nematodes from a fossilized burrow in silt deposits in the Siberian permafrost, she and her colleagues were beyond excited. After thawing the worms in the lab, a radiocarbon analysis of plant material from the burrow revealed that these frozen deposits, 40 meters below the surface, had not thawed since the late Pleistocene, between 45,839 and 47,769 years ago. At the same time, the research group of Teymuras Kurzchalia at the MPI-CBG (Teymuras Kurzchalia is now retired) was already addressing the question of how larval stages of the nematode Caenorhabditis elegans survive extreme conditions. When the team heard about the permafrost nematodes, they immediately reached out for a collaboration with Anastasia Shatilovich.

Vamshidhar Gade, a doctoral student at that time in the research group of Teymuras Kurzchalia, started to work with the permafrost nematodes. "What molecular and metabolic pathways these cryptobiotic organisms use and how long they would be able to suspend life are not fully understood," he says. Vamshidhar is now working at the ETH in Zurich, Switzerland.

The researchers in Dresden conducted a high-quality genome assembly of one of the permafrost nematodes in collaboration with Eugene Myers, Director Emeritus and research group leader at the MPI-CBG, the DRESDEN-concept Genome Center, and the research group of Michael Hiller, research group leader at that time at the MPI-CBG and now Professor of Comparative Genomics at the LOEWE-TBG and the Senckenberg Society for Nature Research. Despite having DNA barcoding sequences and microscopic pictures, it was difficult to determine whether the permafrost worm was a new species or not. Philipp Schiffer, research group leader at the Institute of Zoology, co-lead of the incipient Biodiversity Genomics Center Cologne (BioC2) at the University of Cologne, and expert in biodiversity genomics research, joined forces with the Dresden researchers to determine the species and analyze its genome with his team. Using phylogenomic analysis, he and his team were able to define the roundworm as a novel species, and the team decided to call it "Panagrolaimus kolymaensis." In recognition of the Kolyma River region from which it originated, the nematode was given the Latin name Kolymaensis.

By comparing the genome of Panagrolaimus kolymaensis with that of the model nematode Caenorhabditis elegans, the researchers in Cologne identified genes that both species have in common and that are involved in cryptobiosis. To their surprise, most of the genes necessary for entering cryptobiosis in Caenorhabditis elegans so-called Dauer larvae were also present in Panagrolaimus kolymaensis. The research team next evaluated Panagrolaimus kolymaensis's ability to survive and discovered that mild dehydration exposure before freezing helped the worms prepare for cryptobiosis and increased survival at -80 degrees Celsius. At a biochemical level, both species produced a sugar called trehalose when mildly dehydrated in the lab, possibly enabling them to endure freezing and intense dehydration. Caenorhabditis elegans larvae also benefited from this treatment, surviving for 480 days at -80 degrees Celsius without suffering any declines in viability or reproduction following thawing.

According to Vamshidhar Gade and Temo Kurzhchalia, "Our experimental findings also show that Caenorhabditis elegans can remain viable for longer periods in a suspended state than previously documented. Overall, our research demonstrates that nematodes have developed mechanisms that allow them to preserve life for geological time periods."

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Greenhouse gas release from permafrost is influenced by mineral binding processes

About a quarter of the organic carbon contained in ice-rich Arctic permafrost is more difficult for microorganisms to utilize. The reason for this is a strong binding of the organic material originating from dead plant remains to mineral soil particles. That is the result of a study conducted by a research group led by Professor Dr Janet Rethemeyer and Dr Jannik Martens at the University of Cologne's Institute of Geology and Mineralogy. Accurate predictions of the release of greenhouse gases from permafrost deposits are therefore more complex than previously assumed.

The results of the joint project, which was funded by the German Federal Ministry of Education and Research (BMBF), are published in the article 'Stabilization of mineral-associated organic carbon in Pleistocene permafrost' in the journal Nature Communications.

The Arctic is warming dramatically fast compared to other parts of the world. Much of it is covered by permafrost and contains large amounts of carbon, almost twice as much as the atmosphere. This carbon comes from plants that have grown over thousands of years, decomposed in the soil and then become 'frozen'. Due to strongly rising temperatures in the Arctic, this gigantic freezer is thawing fast. The old carbon stored in it can now be degraded by microorganisms, releasing carbon dioxide and methane into the atmosphere. These greenhouse gases accelerate global warming. The warmer it gets, the more greenhouse gases are in turn released from the permafrost, causing temperatures to rise further and frozen soils and sediments to thaw even faster. "There is a feedback of carbon in permafrost with climate, the strength of which depends largely on those factors that influence microbial degradation," said Janet Rethemeyer.

In the joint research project, scientists from the Institute of Zoology at the University of Cologne, the University of Tübingen, the Technical University of Munich and the Alfred-Wegener-Institute in Potsdam studied long permafrost cores from the Siberian Arctic. The cores come from very ice-rich, fine-grained sediments -- similar to loess in our latitudes -- that were deposited in large areas of Siberia and Alaska during the last ice age. The cores, up to 12 metres long, comprise sediments deposited over a period of up to 55,000 years.

The analyses of the permafrost cores show that a significant part (25-35 %) of the carbon is associated with the mineral particles and thus more difficult to access for microorganisms. "Predictions of interactions between thawing permafrost and climate are very complicated because the microbial degradability of the organic material in the sediments has varied greatly over the last 55,000 years. This is due to the different climatic conditions during this long period of deposition," Janet Rethemeyer explained. Warmer and wetter conditions resulted in poorer binding of carbon to the mineral particles, while a colder and drier climate led to stronger binding, primarily to iron oxides. Stronger binding to iron oxides means that the decomposition rates of old plant material are lower, as Professor Dr. Michael Bonkowski from the Institute of Zoology, Department of Terrestrial Ecology at the University of Cologne has shown in laboratory experiments.

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Ancient DNA found in soil samples reveals mammoths, Yukon wild horses survived thousands of years longer than believed

Mere spoonfuls of soil pulled from Canada's permafrost are opening vast windows into ancient life in the Yukon, revealing rich new information and rewriting previous beliefs about the extinction dynamics, dates and survival of megafauna like mammoths, horses and other long-lost life forms.

In a new paper, published in the journal Nature Communications, researchers from McMaster University, the University of Alberta, the American Museum of Natural History and the Yukon government present a 30,000-year DNA record of past environments, drawn from cored permafrost sediments extracted from the Klondike region of central Yukon.

Researchers used DNA capture-enrichment technology developed at McMaster to isolate and rebuild, in remarkable detail, the fluctuating animal and plant communities at different time points during the Pleistocene-Holocene transition, an unstable climatic period 11,000-14,000 years ago when a number of large species such as mammoths, mastodons and sabre-toothed cats disappeared.

They reconstructed the ancient ecosystems using tiny soil samples which contain billions of microscopic genomic sequences from animal and plant species.

The analysis reveals that mammoths and horses were already in steep decline prior to the climatic instability, but they did not immediately disappear due to human overhunting as previously thought. In fact, the DNA evidence shows that both the woolly mammoth and North American horse persisted until as recently as 5,000 years ago, bringing them into the mid-Holocene, the interval beginning roughly 11,000 years ago that we live in today.

Through the early Holocene the Yukon environment continued to experience massive change. Formerly rich grasslands -- the "Mammoth Steppe" -- were overrun with shrubs and mosses, species no longer held in check by large grazing herds of mammoths, horses and bison. Today, grasslands do not prosper in northern North America, in part because there are no megafaunal "ecological engineers" to manage them.

"The rich data provides a unique window into the population dynamics of megafuana and nuances the discussion around their extinction through more subtle reconstructions of past ecosystems" says evolutionary geneticist Hendrik Poinar, a lead author on the paper and director of the McMaster Ancient DNA Centre.

This work builds on previous research by McMaster scientists who had determined woolly mammoths and the North American horse were likely present in the Yukon approximately 9,700 years ago. Better techniques and further investigation have since refined the earlier analysis and pushed forward the date even closer to contemporary time.

"Now that we have these technologies, we realize how much life-history information is stored in permafrost,"explains Tyler Murchie, a postdoctoral researcher in McMaster's Department of Anthropology and a lead author of the study.

"The amount of genetic data in permafrost is quite enormous and really allows for a scale of ecosystem and evolutionary reconstruction that is unparalleled with other methods to date" he says.

"Although mammoths are gone forever, horses are not" says Ross MacPhee of the American Museum of Natural History, another co-author. "The horse that lived in the Yukon 5,000 years ago is directly related to the horse species we have today, Equus caballus. Biologically, this makes the horse a native North American mammal, and it should be treated as such."

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New research from Arctic: Thawing permafrost peatlands may add to atmospheric CO2 burden

Temperatures in the Arctic are rising twice as fast as in the rest of the world, causing permafrost soils to thaw. Permafrost peatlands are biogeochemical hot spots in the Arctic as they store vast amounts of carbon. Permafrost thaw could release part of these long-term immobile carbon stocks as the greenhouse gases carbon dioxide (CO2) and methane (CH4) to the atmosphere, but how much, at which time-span and as which gaseous carbon species is still highly uncertain.

A new study led by researchers from the University of Eastern Finland and the University of Montreal, in cooperation with researchers from various Nordic research institutions, finds that peatlands may strengthen the permafrost-carbon feedback by adding to the atmospheric CO2 burden post-thaw. The study was recently published in Global Change Biology -- a leading journal in environmental science.

By applying a novel experimental approach using intact plant-soil systems (mesocosms), the authors were able to simulate permafrost thaw (thawing of the upper 10-15cm of permafrost) under near-natural conditions. Greenhouse gas flux dynamics were monitored via high?resolution flow?through gas measurements, combined with detailed monitoring of soil greenhouse gas concentration dynamics, yielding insights into gas production and consumption potential of individual soil layers. The study finds that under dry conditions, peatlands may strengthen the permafrost-carbon feedback by adding to the atmospheric CO2 burden post-thaw. However, as long as the water table remains low, the results reveal a strong CH4 sink capacity in these types of Arctic ecosystems pre? and post?thaw, with the potential to compensate for part of the permafrost CO2 losses over longer timescales.

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Greenhouse emissions from Siberian rivers peak as permafrost thaws

Western Siberia.

As permafrost degrades, previously frozen carbon can end up in streams and rivers where it will be processed and emitted as greenhouse gases from the water surface directly into the atmosphere. Quantifying these river greenhouse gas emissions is particularly important in Western Siberia -- an area that stores vast amounts of permafrost carbon and is a home to the Arctic's largest watershed, Ob' River.

Now researchers from Umeå University (and collaborators from SLU, Russia, France, and United Kingdom) have shown that river greenhouse gas emissions peak in the areas where Western Siberian permafrost has been actively degrading and decrease in areas where climate is colder, and permafrost has not started to thaw yet. The research team has also found out that greenhouse gas emissions from rivers exceed the amount of carbon that rivers transport to the Arctic Ocean.

"This was an unexpected finding as it means that Western Siberian rivers actively process and release large part of the carbon they receive from degrading permafrost and that the magnitude of these emissions might increase as climate continues to warm" says Svetlana Serikova, doctoral student in the Department of Ecology and Environmental sciences, Umeå University, and one of the researchers in the team.

Quantifying river greenhouse gas emissions from permafrost-affected areas in general and in Western Siberia in particular is important as it improves our understanding the role such areas play in the global carbon cycle as well as increases our abilities of predicting the impacts of a changing climate on the Arctic.

"The large-scale changes that take place in the Arctic due to warming exert a strong influence on the climate system and have far-reaching consequences for the rest of the world. That is why it is important we focus on capturing how climate warming affects the Arctic now before these dramatic changes happen" says Svetlana Serikova.

From Science Daily

'Abrupt thaw' of permafrost beneath lakes could significantly affect climate change models

Methane bubbles are trapped in the ice on a pond near Fairbanks, Alaska.

Methane released by thawing permafrost from some Arctic lakes could significantly accelerate climate change, according to a new University of Alaska Fairbanks-led study.

The study, which was published Aug. 15 in the journal Nature Communications, focuses on the carbon released by thawing permafrost beneath thermokarst lakes. Such lakes develop when warming soil melts ground ice, causing the surface to collapse and form pools of water. Those pools accelerate permafrost thaw beneath the expanding lakes, providing food for microbes that produce the greenhouse gases carbon dioxide and methane.

Lead author Katey Walter Anthony and her colleagues studied hundreds of thermokarst lakes in Alaska and Siberia during a 12-year period, measuring their growth and how much methane was bubbling to their surface. By combining field work results with remote-sensing data of lake changes during the past two years, they determined the "abrupt thaw" beneath such lakes is likely to release large amounts of permafrost carbon into the atmosphere this century. The lake activity could potentially double the release from terrestrial landscapes by the 2050s.

The effort, conducted by a team of U.S. and German researchers, is part of a 10-year NASA-funded project to better understand climate change effects on the Arctic. Additional support by the National Science Foundation allowed scientists from UAF and the Alaska Division of Geological and Geophysical Surveys to collect data on permafrost location, thaw and associated greenhouse gas release from lakes in Interior Alaska's Goldstream Valley.

The researchers found the release of greenhouse gases beneath thermokarst lakes is relatively rapid, with deep thawing taking place over the course of decades. Permafrost in terrestrial environments generally experiences shallow seasonal thawing over longer time spans. The release of that surface permafrost soil carbon is often offset by an increased growth in vegetation.

"Thermokarst lakes provide a completely different scenario. When the lakes form, they flash-thaw these permafrost areas," said Walter Anthony, an associate professor with UAF's Water and Environmental Research Center. "Instead of centimeters of thaw, which is common for terrestrial environments, we've seen 15 meters of thaw beneath newly formed lakes in Goldstream Valley within the past 60 years."

Emissions from thermokarst lakes aren't currently factored into global climate models because their small size makes individual lakes difficult to include. However, the study's authors show that these lakes are hotspots of permafrost carbon release. They argue that not including them in global climate models overlooks their feedback effect, which occurs when the release of greenhouse gases from permafrost increases warming. That feedback is significant because methane is about 30 times more potent than carbon dioxide as a heat-trapping gas.

Existing models currently attribute about 20 percent of the permafrost carbon feedback this century to methane, with the rest due to carbon dioxide from terrestrial soils. By including thermokarst lakes, methane becomes the dominant driver, responsible for 70 to 80 percent of permafrost carbon-caused warming this century. Adding thermokarst methane to the models makes the feedback's effect similar to that of land-use change, which is the second-largest source of human-made warming.

Unlike shallow, gradual thawing of terrestrial permafrost, the abrupt thaw beneath thermokarst lakes is irreversible this century. Even climate models that project only moderate warming this century will have to factor in their emissions, according to the study.

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