New methane-belching microbe found in Alaska permafrost

Doug O'Harra
Photo courtesy Christopher Arp, USGS

Genetic analysis of Interior Alaska permafrost has uncovered what may be the state's newest creature -- a methane-producing microbe so tiny that a billion of them could fit inside a teaspoon of freshly thawed muck.

This wee archaean methanogen, as yet unnamed, was unearthed during a high-tech investigation into how greenhouse gas-spewing microscopic life in Arctic soils might respond once their tightly frozen world transforms into ripe-smelling slurry. One answer: it doesn't take long for this microbial legion to start belching away, so to speak.

"In just a matter of days, the microorganisms were shifting their community -- the functions were shifting and starting to behave more like a seasonally thawed active layer (of summertime permafrost)," explained Janet Jansson, a microbial ecologist, and one of the study's eight authors, from Lawrence Berkeley National Lab in California. "It happened very rapidly."

As this dirt-constrained universe exploded to life within sealed labratory samples, among the most prolific appeared to be the new organism, comprising about 2 percent of the genetic mix. Scientists believe this novel creature may be responsible for the sudden and dramatic release of the super-greenhouse gas methane observed during the study.

"It was pretty abundant," Jansson explained in a phone interview. "Our hypothesis is that the methane accumulating in the permafrost was produced by this organism that we discovered. If it thaws, (methane) is released to the atmosphere."

The project marked the first time scientists had identified a draft genome of a new soil organism using these particular methods -- which involved gathering and then sequencing billions of bits of genetic material. The unknown organism also appeared to be fixing nitrogen, another first, the scientists said. 

The study, published online by the journal Nature, is part of a broader scientific effort to understand what will happen as the Arctic’s extensive permafrost thaws for longer periods and to greater depths in response to warming conditions. The region may become one the most important new sources of greenhouse gases, with uncounted trillions of mostly unknown and never-seen Arctic microbes suddenly playing an outsized role in global climate change.

The new study took a unique, penetrating glimpse into what Jansson calls "the Earth's 'dark matter.'

"These detailed analyses reveal for the first time the rapid and dynamic response of permafrost microbial communities to thaw," the scientists wrote. "The thaw-induced shifts that we detected directly support conceptual models of carbon and nitrogen cycling in Arctic soils, in which microbes play a central role in greenhouse gas emissions and destabilization of stored permafrost carbon."

Methane time bomb ticks inside permafrost

Within the layer of permanently frozen ground beneath Alaska and the Far North -- reaching to depths that exceed 1,000 feet -- is a vast quantity of frozen organic matter deposited and preserved over eons. Scientists estimate that there might be more than 1.6 trillion metric tons of carbon sequestered in this permafrost -- containing as much carbon as found in all of the Earth's plant life and atmosphere combined. That's more than 250 times the amount of fossil fuel emissions spewed by every car, truck, train, factory and power plant in the United States in 2009.

As the Arctic climate warms, more permafrost will thaw, allowing an ever-increasing proportion of its organic stash to molder and decay.

"The permafrost is poised to become a major source of greenhouse gases as the temperature in the Arctic is expected to increase dramatically compared to the expected temperature increase in other regions of the world," Jansson explained in this story.

So where do the microbes fit in?

Trapped inside every dime-size hunk of permafrost are billions of tiny organisms from hundreds or thousands of species, most of them completely unknown to science. Many of these strange creatures are single-cell archaeans, members of a weird and sometimes extreme kingdom of life on Earth that’s distinct from bacteria, protozoa, plants and animals.

They exist in an ecosystem scaled in microns -- an inner-space beneath our feet inhabited by alien beasties only about 39 millionths of an inch in length. In permafrost, their habitats become microscopic ponds or films of very salty water, squeezed into existence between the grains by the freezing action of soil water.

It's within these almost unimaginably tiny bodies of brine that soil microbes eek out their constricted existence.

"It's going to be very heterogeneous, with soil particles of different sizes that make little pores that they have to get through, and then you have plugs of organic materials that they have to somehow maneuver around," Jansson explained.

Still, the creatures remain active -- chomping organic matter and producing greenhouse gas as a by-product -- even at subzero temperatures, she said. "It’s just that their activity rates are so slow."

Meltdown jumpstarts microscopic activity

To find out what happens when this microscopic world thaws and the archaean party gets rowdy, the team focused on samples of permafrost collected near Hess Creek, a Yukon River tributary north of Fairbanks. Co-author Mark Waldrop, a soil scientist with the U.S. Geological Survey, gathered meter-deep cores from black spruce peat and sent them south for analysis. The samples were incubated at about 41 degrees F, sent to Jansson and her team for DNA extraction, and then to Eddy Rubin and Rachel Mackelprang at the U.S. Department of Energy Joint Genome Institute to be genetically sequenced.

To sort out what critters might be present, scientists had to process nearly 40 billion bases of raw DNA sequence, the scientists said.

"These microbial communities are extremely diverse," explained Mackelprang in this story about the project. "A single gram of soil may contain thousands of different bacterial species and billions of cells. Additionally, most of these microbes cannot be grown in the laboratory, making this an extremely difficult area to study."

Among other things, the scientists discovered a bacterium that eats methane while releasing CO2, as well several microbes that produced methane, including the new methanogen.  

The ultimate goal of this line of research will be to help climate modelers better understand the role these microrganisms play in the production of greenhouse gases, Jansson said. It’s not a simple issue.

"As the permafrost thaws, they have the possibility to become active and degrade it and release methane and CO2," she explained. But "some of those organisms are methane consumers, and some are methane producers, and so, the absolute net amount of methane that is released is going to be dependent on the dynamic of those populations in the soil."

As for Alaska's newest soil denizen, not much is known yet. "We didn't ever get a chance to look at it, you know," Jansson said. "From the DNA information, we were able to reconstruct the genome. But we never saw it. … We have no idea what it looks like."

Most of these archaeans tend to resemble strange rods and fuzzy spheres, she added.

Still, without an isolated sample in hand, Jansson and her colleagues don’t get the privilege of naming their new bug. Although pinpointing individual species of soil microbes can be exceedingly difficult -- and breeding up a fresh batch even harder -- it can be done.

The next step? "Maybe that’s what we should do," Jansson said.

Contact Doug O'Harra at doug(at)