Finding Needles in the Permafrost

Approximately 20% of the earth’s land surface is covered by permafrost, soil that remains permanently frozen throughout the seasons. It is found mainly at the poles in the Arctic and Antarctic tundra, and acts as a gigantic carbon reservoir: with an estimated 1.7 trillion tons of carbon, permafrost contains 57 times the amount of carbon that is annually released by anthropogenic sources into the atmosphere. The continued emission of man-made greenhouse gases, such as carbon dioxide released by burning fossil fuels, contributes to global warming. Rising temperatures, in turn, are expected to cause a significant proportion of permafrost to thaw, with unknown consequences for the organic matter trapped within. Will the carbon that has been locked up in permafrost for millennia be released into the atmosphere immediately, or will microbial communities in the soil metabolize it and slow down its release? How will the complex ecosystem of microorganisms, plants, and animals respond to a thaw?

Credit: Brocken Inaglory

To gain insight into these questions, a team of researchers led by Janet Jansson, professor and senior staff scientist in the ecology department at Lawrence Berkeley National Laboratory (LBL), analyzed the effect of thaw on microbial permafrost communities from Hess Creek, Alaska. Soil at Hess Creek is known to be rich in organic matter, making it an ideal candidate to study the release of greenhouse gases upon thaw. Samples for the study were collected by Mark Waldrop, a research scientist at the United States Geological Survey, who extracted soil cores to a depth of 1 m, containing both the permafrost and its overlying, ~35 cm thick, seasonally thawed active layer. The soil samples were kept frozen until their arrival at Jansson’s laboratory at LBL, where they were allowed to thaw while the release of gases was monitored. Whereas the active layer mainly released carbon dioxide upon thaw, there was a burst of methane from the permafrost sample. Methane is more effective than carbon dioxidein reflecting radiation in the atmosphere, making it one of the most potent greenhouse gases. Its release upon thaw can trigger a positive feedback loop, explains Jansson: “As permafrost thaws, microorganisms degrade carbon, and greenhouse gases such as carbon dioxideand methaneare released. Their release, in turn, aggravates global warming, which then causes more permafrost to thaw.”

To identify microbial species present in permafrost and the genes responsible for methaneproduction and consumption, Rachel Mackelprang, a postdoctoral fellow at LBL and the Joint Genome Institute at the time, extracted DNA from the soil samples and sequenced it, an approach known as metagenomics. In contrast to conventional DNA sequencing, where DNA from a single, isolated species is examined, metagenomics targets complex environmental samples that contain a mixture of DNA from different organisms. Metagenomics can therefore reveal the diversity of a habitat, which is often overlooked when only species that can be grown in the laboratory are sequenced. Performing metagenomics on the permafrost sample from Hess Creek was challenging: its soil is highly diverse, the overall cell density is low, and its bacteria tend to form “pseudospores,” a dormant state with a tough outer shell that makes them resistant to extreme environmental conditions, and also to lysis in the lab. To obtain sufficient amounts of DNA for metagenomic sequencing, Mackelprang had to rely on a novel way to amplify DNA, using so-called emulsion polymerase chain reaction to individually amplify small fragments of DNA. Sequencing of these fragments produced almost 40 billion bases of DNA sequence – a phenomenal success and huge challenge at the same time. “First you think that’s fantastic, because you get so much sequence data, but it can be a challenge to assemble it, and to make sense of it,” says Jansson. However, the metagenomic sequencing data turned out to yield a large number of long DNA assemblies. To the researchers’ surprise, they even achieved the assembly of a draft genome for a novel methane-producing microorganism. “We definitely didn’t expect to get that from our analysis of this soil sample – it is really fascinating that it worked at all,” says Jansson.

The scientists then mined their data to study relative changes of genes known to be involved in carbon and nitrogen cycling. On the basis of observed increases and decreases of these genes upon thaw, they proposed a model of carbon and nitrogen cycling between the permafrost, the active layer and the atmosphere. When Jansson showed her model to a climate scientist at LBL, she discovered that their metagenomics analysis confirmed existing theoretical models of carbon and nitrogen cycling. “We did not know what their models looked like when we analyzed our data,” says Jansson. “The agreement between the data lends a lot more confidence to our approach.” The model predicts that part of the methaneproduced by microbes in the permafrost is depleted by methane-consuming bacteria, but a portion of it is released into the atmosphere along with other greenhouse gases such as carbon dioxide and nitrous oxide. The remaining key question is whether these greenhouse gases can be trapped by other microorganisms as well as plants, which would be expected to thrive with rising temperatures. These complex interactions are the focus of a new collaborative study initiated by the Department of Energy, termed Next-Generation Ecosystem Experiments. The experiment will run over a period of 10 years and draw on the expertise of hydrologists, biogeochemists, geophysicists, climatologists and microbiologists to gain a better understanding of the complex permafrost ecosystem and its response to climate change.

Susanne Kassube is a graduate student in biophysics.