She unearths diversity in the soil

Ninety percent of the world’s fungi are invisible to us, hidden in a widely ramified underground society. But one of these mysterious fungi systems is now being examined using a new method by evolutionary biologist Anna Rosling.

It may come as a surprise that small organisms like fungi are so influential in terms of life both above and below ground. But the fact is that fungi significantly affect not only each other, but also roots, plants, trees – even the earth’s atmosphere. What makes fungi so successful is something Anna Rosling wants to find out.

“Fungi societies are very dynamic systems,” says Anna Rosling. “The vast majority of fungi don’t form any fruiting bodies so you never see them above the ground. But they live down there and can completely dominate and drive processes such as breaking down carbon, absorbing phosphorus and making nitrogen available to the trees.”

Underground, fungi intermingle with numerous species of animals, insects and roots. How the fungi manage to adapt and interact with the soil to survive and reproduce is a question Anna Rosling has explored her entire research career.

“In my dissertation in 2003, I examined stone weathering, how fungi can alter stones and absorb nutrients from them. Since then, my interest has shifted to the soil as a biological system. How have the fungi adapted to the roots of different plants and different types of nutrients? I’m trying to understand the importance of biological interaction in comparison with adaptation to a physical environment in the processes that lead to the high diversity of the fungi societies.”

Fungi DNA analysed

To document soil fungi societies, Anna Rosling’s team uses several different molecular methods. DNA or RNA is extracted from soil samples and analysed by the researchers. Different types of phosphorous can provide important answers on nutrient conditions in the soil. The researchers also isolate fungi from spores and roots to run controlled experiments in the lab.

“We do the sequencing at SciLifeLab in Uppsala,” says Anna Rosling. “But here at the Evolutionary Biology Centre, we have the equipment to extract and copy DNA. We can then see which genes the fungi expresses and which species complex dominates, and thus begin to understand the soil system.”

In a new project financed by the European Research Council, ERC, she will study a long-disputed fungi group. The arbuscular mycorrhiza fungus, or AM fungus, has its origin about 470 million years ago and is believed to be the foundation of the plant kingdom’s colonisation on Earth. AM fungi consist of hundreds of species that form mycorrhizas with grass, flowers and ordinary plants. Anna Rosling’s team is now working to take samples and isolate fungi from Uppsala Kungsäng, an old meadow with well-documented flora since the time of Carl Linnaeus.  

“Almost all of the plants have mycorrhiza, which means ‘fungus root’. They need these for their nutrition and to stay healthy. In the mycorrhiza, or symbiotic association of a fungus and roots, the fungi provide nourishment to the plant in exchange for energy. But some combinations of fungi and plants don’t work as well as others. What I am curious about is if the plant chooses its mycorrhiza and if the mycorrhiza chooses its plant. In the new ERC project, we’ll be studying how the fungi’s composition of genomes affect their ability to choose plants.”

Spore nuclei organisation can solve the riddle

The reason that AM fungi have long been the subject of scientific debate is that these fungi, unlike most organisms, do not exhibit any sexual stage with a cell nucleus. Instead, they reproduce through large spores with hundreds of nuclei in each, which have proven to have a high degree of genetic diversity. The question the researchers are asking is how AM fungi genomes are organised and are able to remain competitive.

“There is a hypothesis that they have different nuclei in them, so that they are actually like a small society or a population,” says Anna Rosling. “In this way, they manage the variations within themselves, instead of between themselves.  And then there are new findings saying that AM fungi are just like regular fungi, that they must have a sexual cycle somewhere. But this debate has gone on a long time and I have developed a method for solving it.”

The method of documenting the fungi’s genomic systems is still under development, so she can’t reveal any details. But it is clear that the work to investigate the mycorrhiza’s spore nuclei will largely take place at the single-cell genomics platform at SciLifeLab. This platform has the genetic engineering resources, particularly the staff. But even if the method has already shown promise in pilot studies, Anna points out that the lab is an engineered environment. 

“When you do experiments, you really have to ask if this is relevant. Is this a situation that occurs in real life? Because we create a lot of scenarios in  the lab where something else significant could take over. But that’s also what’s fun about soil systems – they’re so complicated.”

Anna Rosling’s research team will also work with her previous colleagues at the Swedish University of Agricultural Sciences, SLU. She and the new doctoral students will also conduct several studies at Indiana University Bloomington and the University of Kansas in the US, which have many years of experience researching AM fungi systems.

What drives you as a researcher?

“I think that I’m very interested in things, I can latch onto something and hold on a long time. The method of researching is also really fun – finding out how something works from the ground up.
What I especially like about research is that you create new knowledge. First we don’t know – and then we know.”

Anneli Björkman