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Dark fungi in the roots can be important players in the forest ecosystem

Published: 16 February 2024
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Among the roots of trees, fungi and bacteria live in a complex web of different types of interactions. In the roots, we find fungi with dark-coloured hyphae that appear to play an important, previously overlooked role in the ecosystem, according to a recent article by SLU researcher Tarquin Netherway and his colleagues. A large field study suggests that they have implications for both plant health and carbon and nutrient cycling.

Trees as long lived stationary organisms rely heavily on relationships with microorganisms to meet their nutrition needs for growth and survival, with the seemingly most important relationships being between trees and mycorrhizal fungi.

Common but unknown

While a lot of attention has been given to the importance of mycorrhizal associations in plant-soil interactions, little attention has been paid to the potential importance of other common and widespread root-dwelling fungi such as dark septate endophytes. You may be wondering what that is? Well, an endophyte is an organism that lives inside another organism. They are dark because they produce melanin, the same pigment you have in your skin. 'Septate' means that the hyphae of the fungus have barriers between the cells; in some fungi, the hyphae are just long tubes without barriers, essentially a single cell.

These fungi have been most studied in agricultural systems, where they appear to confer their hosts with enhanced stress tolerance. However, dark septate endophytes occur in the roots of different kinds of plants in many ecosystems, including common trees and forests.

Ecologically important

Fungi living at the interface between roots and soil can affect the interaction between plants and freely living microorganisms and directly influence the structure and function of root and soil microbiomes. This includes ecologically important organisms such as plant pathogens, nutrient transforming microbes, and saprotrophs.

Untangling how these truly small but important organisms interact is not easy, and that is where Tarquin Netherway's research comes in.

Large field study

He conducted a large field study in Europe at 18 sites from northern Norway down to central Italy. During the summer of 2019, they collected root samples from common tree species, including birch, alder, and rowan. The aim was to analyse which fungi had colonized the roots. They also took soil samples and analysed them using DNA methods to find out which microorganisms lived in the soil.

“We had expected mycorrhizal symbioses to be important in explaining the properties of thebelow-ground microbiome. But to our surprise, we found a stronger association with dark septate endophytes,” says Tarquin Netherway.

Fewer pathogens

In the roots and surrounding soil there were fewer pathogens when there were more dark septate endophytes. There were also relatively fewer bacteria compared to fungi when the roots contained these dark fungi, which are common in ecosystems with slower nutrient turnover and harsher environments. Additionally, the microorganisms sampled had fewer genes related to nutrient cycling. This is generally the case in nutrient-poor environments.

“These are exciting results because they potentially have significant implications for carbon and nutrient cycling and plant health in many ecosystems. I hope that these results will highlight dark septate endophytes and stimulate new interesting discoveries,” says Tarquin Netherway.

Fascinating subject

Dark septate endophytes fascinate him. They are not entirely dependent on tree roots and can live freely in the soil. But they are very difficult to detect there. DNA analysis does not help because it is not a well-defined group of fungi. Being a dark septate endophyte is more of a lifestyle. For example, there are fungi that form mycorrhiza with heather plants (ericoid mycorrhiza), but they appear as dark septate endophytes on other plants.

Tarquin will now continue to study the role of root-associated fungi in shaping plant and soil microbiomes. He is interested to dive deeper into the ecology of dark septate endophytes. What mechanisms can explain their seemingly pervasive role in plant-soil interactions?

“It is not known exactly what these dark septate fungi do - they probably benefit from the plants and perhaps also give something back, such as protection against disease and stress,' says Tarquin.

In particular, Tarquin is interested in studying the role of melanin production by dark septate endophytes in ecological interactions with other fungi, bacteria, and plants.

 Person taking a soil sample in the forest.

Tarquin Netherway in field. Photo: Anna Lundmark

Scientific article

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe, Nature Communications