The life hidden within the thawing permafrost: how does climate change affect microbes?

The balance of power between microbes living in the Arctic region might be a matter of life and death also to humans. It determines how much methane is released by the thawing permafrost.

After a research group meeting, the whiteboard in Jenni Hultman’s office has a message scribbled on it in block letters: “JENNI MIGHT CONSIDER HEADING TO THE LABORATORY!” After all, in the freezer of the laboratory there are samples drilled from the surroundings of the Kilpisjärvi Biological Station just waiting for her to get to work.

“You could say that they tell a story about the future,” says Hultman, who is a microbiologist by profession and an Academy of Finland research fellow.

Hultman’s group focuses on microbes in the Arctic soil and how changes in conditions affect the ways bacterial communities function. The researchers’ goal is to extract and compile microbial genes from the soil samples. They also wish to determine which microbial genera are active and which of them are dormant.

Increasing moisture

Researchers have established a network of measuring sites across the Saana fell in Kilpisjärvi. The samples collected from the drier sites have already been analysed, but some of the samples from the wetter areas are still waiting for their turn. They point to the future in the sense that the progress of climate change is likely to make the Arctic region even wetter – on average.

However, although changes are expected, no one is certain about the details. The organisms Hultman specialises in are among the greatest sources of uncertainty. When microbes break down organic layers of soil, they produce and gradually release carbon dioxide, methane, nitrous oxide, and other greenhouse gases into the air. However, there are also bacteria which make use of methane by oxidising it.

But which of these microbes are winning, the carbon eaters or the carbon emitters – the suppressors of climate change caused by humans or those speeding up the problems? This is the key question at Hultman’s laboratory.

Which species are the most active and dominant in the current conditions, and which species benefit from warmer air and soil, shorter winters, the thawing of permafrost, nutrients released from under the ice and increased moisture?

A crucial carbon reservoir

Unanswered questions on the path towards the right answers are as abundant as the blanket of snow over the Saana fell in the winter. How to determine the impact of changing conditions when we know so little of soil microbes overall? Their mutual interaction is even more of a mystery.

Yet these questions must be tackled, as the answers to them are vital, Hultman points out. There is a gigantic carbon reservoir under the Arctic permafrost: twice the amount of the carbon in the atmosphere, more than the carbon stored in all of the forests across the globe. The future of the planet hangs in the balance.

“We can’t say that our research will uncover even the tip of the iceberg. It’s only a small fraction we are talking about. We are not targeting individual bacterial species. Instead, our analyses are carried out on the level of bacterial genera and families, as even those number in the tens of thousands.”

Still, important discoveries have already been made.

“All across the Arctic region, microbial species appear to be relatively uniform. Whether in Alaska or Kilpisjärvi, DNA analyses point to only minor differences. The bigger differences lie in the RNA – that is, which microbes are active in various environments.”

Pleasant surprises

The samples which were analysed first revealed pleasant surprises: there were more bacteria that utilise methane than expected.

However, Hultman is expecting bleaker results from the analyses of the samples originating in the wet measuring sites. Earlier, she has weeded through sample series collected in Alaska, specifically melting gradients, and believes those findings also give clues about the situation in Kilpisjärvi.

“With the permafrost thawing fast, the warming soil has no time to become forested. Instead, it collapses into what is known as thermokarst wetlands, resulting in a significant increase in greenhouse gas production. Moist, oxygen-free conditions are favourable to species that emit methane.”

According to Hultman’s assumption, the microbial communities currently living around Kilpisjärvi take it fairly easy for most of the year. They only get busy when the nutrient-rich meltwaters are released in the early summer.

“The circumstances prevalent during the most intense period of growth constitute an interesting research question.”

One of the surprises sprung on the researchers by the fell environment has been the great quantity of Thaumarchaea, which are poorly known organisms, found in the soil. Only recently, archaea were considered organisms that only live in geysers and other similar extreme conditions.

“Our observations speak of the diversity of the organisms living in the soil, something that remains relatively unknown to science.”

A nitrogen reservoir and a hammer

RNA analyses, which expose microbial activity, are labour-intensive compared to DNA analyses. Hultman and her group have traversed the fell carrying liquid nitrogen containers to capture real-life variants in real time by freezing them.

“I always tell my students that you shouldn’t give into gazing at RNA, as it breaks up quickly.”

The coldest freezer at the Kilpisjärvi Biological Station serves as the interim storage, and liquid nitrogen is again used for transporting the samples to Helsinki. At the laboratory in Viikki, the analyses are carried out under deep cryogenic conditions produced by dry ice.

The work involves the use of heavy-duty hammers.

The earthworm effect

Hultman wants to subject the exactly same samples to both RNA and DNA analyses.

“Even the slightest local changes in the terrain have an impact on the abundance of microbial species: there may be a dead earthworm sprawled on the ground in one place, while in another the root of a plant leaking lots of carbon into the soil is snaking through. Both could have great significance.”

Above her desk, Hultman has attached an aerial image printed out from a map application. The colour is musty green, but Hultman is happy and proud of this window to the landscape immortalised in the picture. The 118 measuring sites flecking the map are a good way to understand the nuances of the natural fell environment.

Hultman and her colleagues are drilling samples from two different depths at each site; from the five-centimetre deep organic surface layer and deeper, from the mineral soil, the rocky flank of the fell permitting.

The sites were established to serve a research group headed by Professor of Geography Miska Luoto, but they are also a perfect match for biologists. Through shared efforts, the researchers regularly keep tabs on the temperature, acidity and moisture of the measuring sites.

Survival through dormancy

Hultman’s term as an Academy of Finland research fellow and her sample analysis will continue until 2022. In other words, more answers to the unanswered questions are on the horizon, but some observational outlining can be done already.

“Most bacteria are tough basic species, while opportunistic bacterial families are in the minority. However, we cannot focus solely on the most active species, since new conditions may bring forward unforeseen dark horses,” Hultman assesses.

There will be extinctions too, even though the resilience of microbes is admirable: many species survive even violent change by lying dormant.

The article has been published in Finnish in the 2/2020 issue of Yliopisto magazine.

A new field

Genetic research focused on the functioning of microbial communities has established a new discipline, metagenomics, in the field of biosciences. Communities studied as a whole are so complex that they cannot be cultured in laboratory conditions by mimicking genuine growth conditions. Instead, the work has to be done by analysing all the genetic material found in the samples collected in the field.

The study of community activity, RNA analyses included, is known as metatranscriptomics.

Investigating microbial communities through RNA analyses is fairly rare globally. One of the partners of the research group active at the University of Helsinki is the United States Geological Survey, which employs biochemists and geologists specialised in the permafrost area of Alaska.