Studying soil fungal dynamics using sequencing methods

Andreas Schneider, PhD student at the Department of Plant Physiology at Umeå University.

ImageLaura Hinojosa

Our experiments show that small amounts of organic nitrogen fertilization can improve the survival and growth rates of seedlings but do not affect the fungal community,

Studying fungal communities in the forest soil is very challenging. The mushrooms seen in the forest in autumn are just made by some of the fungi to spread their spores. The most time of their lifecycle fungi are hidden in the soil or inside of the roots of their host plants.

New methods show the dynamic

Recently developed advanced sequencing techniques offer many new possibilities and Andreas Schneider and his colleagues used these advances to develop automated bioinformatic tools that allow to study the dynamic and diversity of fungal communities in the soil.

“Many of the methods used to study fungi today are indirect. We extract DNA from a soil sample and then see to which species this DNA might belong to,” explains Andreas Schneider, PhD student at the Department of Plant Physiology at Umeå University.

Andreas Schneider used these methods in some of his studies, but one problem is that DNA is very stable which makes it difficult to know if the DNA comes from dead or living organisms. That is why he used and further developed additional methods based on RNA sequencing that show how active the fungi are and which of their genes are being expressed.”

Nitrogen application changes the fungal community

To test the method, Andreas Schneider analysed how nitrogen addition affects the fungal community. Swedish forests are usually low in nitrogen and conifer trees compensate for this limitation by establishing the symbiosis with mycorrhizal fungi. The trees deliver carbon to the fungi and receive nitrogen in return. For seedlings on reforestation sites, it is crucial to establish the connection with the fungi to improve their chances to survive.

Nitrogen addition, especially in high doses, is already known to change the fungal community in the soil quite a lot.

“Our experiments show that small amounts of organic nitrogen fertilization can improve the survival and growth rates of seedlings but do not affect the fungal community,” says Andreas Schneider. “This was true for seedlings coming from nurseries and also for seeds that were directly placed on the field site. We still need to follow up on the seedling growth rates over a longer period of time and for more different local conditions, but the current results are very promising.” 

In a different approach, Andreas Schneider analysed how nitrogen addition inhibits the degradation of lignin in forest soils. Lignin is one main component in dead plant material that is decomposed slowly by white-rot fungi.

Andreas Schneider could show that nitrogen addition changes chemical processes in the soil which makes the degradation of lignin less efficient and reduced the activity of white-rot fungi. He could also confirm that the composition of the fungal community associated with tree roots is changed on sites with high nitrogen towards more nitrogen tolerant fungi species and that this can be caused both by changes of the soil chemistry changes and by a reprogramming of the mycorrhizal symbiosis from the side of the host tree.

Lack of genetic information

“We could show that our methods are working and are useful to study dynamic changes in the fungal community”, thinks Andreas Schneider. “The biggest limitation now is the lack of genetic information for most fungal species, but we and many others are working on that. I am sure that in the future, this new knowledge and these methods will help us to evaluate even better how different forest management strategies influence fungal activity and biodiversity.”

Andreas Schneider was part of the PhD Research School in Forest Genetics, Biotechnology and Breeding and collaborated for his PhD project with Holmen Skog.