A Forest of Fungi: Detangling the Plant Mycobiome

Tuesday, February 25, 2020
In the race against global climate change, researchers at the University of Arizona are working to preserve, catalog, and map the potential of thousands of species of imperiled fungi found in the world’s boreal forests.

Fungi are responsible for some of the world’s greatest advances, from penicillin and cancer treating drugs to pest control and food production. But while scientists estimate there are anywhere from 1.5 to 5.1 million species of fungi, the majority of these unknown species are hidden symbionts inside of plants. Thus, the true diversity, function, and potential applications of the fungal microbiome, or “mycobiome,” remains largely untapped.

As climate change calls the future of the world’s forests into question, researchers at the University of Arizona are in a race against the clock to preserve and characterize thousands of species of endangered fungi, which they believe may hold the key to understanding how forests will survive and adapt to a hotter, drier future.  

“As our climate warms and as these species and their ranges are being restricted, we’re losing not only the genetic diversity of plants but also their symbionts,” said Jana U’Ren, an assistant professor of ecosystem genomics in the University of Arizona Department of Biosystems Engineering and BIO5 Institute.

“The challenge of working with these organisms is that we can’t see them. So, if you look outside and look at the plants, you would never know that they have thousands of symbionts that are likely helping them survive.”

All plants on earth harbor symbiotic fungi in their leaves, roots, and other tissues, each playing an important role in plant health, but there is still a lot unknown about how they support their hosts under stress.

On a mission to detangle the role these fungi play in forest resilience, U’Ren, as a postdoctoral researcher within Betsy Arnold’s lab at the UArizona School of Plant Sciences, studied how endophytes—particularly the fungal mycobiome in leaves—are distributed on a global scale.

Together with an interdisciplinary team of scientists from Duke University, North Carolina State University, University of San Francisco, and the University of Minnesota, Arnold and U’Ren focused in on Boreal forests, which represent the world’s largest terrestrial biome.

“Boreal forests are threatened by climate change and are enormously important in the Earth’s carbon cycle,” said Betsy Arnold, a lead scientist on the NSF-funded Dimensions of Endophyte biodiversity project.

“We had preliminary evidence that there is a tremendous evolutionary diversity of endophytes in these imperiled forests, and as a first step to understanding their functional roles and vulnerability to climate shifts, we needed to understand how they are distributed.”

Are the endophytes in Boreal forests similar to those in other plant communities and can a given fungal symbiont use any plant host or are they particular to a specific host? And most importantly, how are these endophyte communities sensitive to climate?

Over a three-year period, the Endophyte Biodiversity team collected nearly 500 host plants in seven forest field sites, spanning boreal forests in the Russian Far East, Sweden, Canada, and the United States. From this host material, fungi were isolated in culture and identified using DNA sequencing. Because many fungi will not grow in the lab, U'Ren also used high-throughput DNA sequencing methods to identify all of the fungi inside the plant leaves.

Their findings, published late last year in Nature Ecology and Evolution, show that endophytes in Boreal forests are globally unique and quite different from those found in other biomes or soils.

“We show that boreal endophytes are sensitive to climate, but they are even more sensitive to the availability of their hosts,” Arnold said. “If their hosts—spruces, mosses, even lichens—are lost due to climate change, then this immense biodiversity may disappear.”

The project generated over 11,000 cultures, the largest data set ever collected for a project of this scale, that are now housed in the UArizona Mycological Herbarium as a living repository of this diversity.

In their single study, U’Ren and Arnold observed well over 6000 endophyte species, with an estimated 95% or more that are expected to be new to science.

“Now that we’ve preserved that diversity, we’re delving more into their genomes, looking specifically at how they are helping plants,” U’Ren said. “Some of these fungi produce compounds that are really important for medicine, new anti-microbial compounds, new anti-cancer compounds. So, this is a huge genetic resource for many fields, including medicine and agriculture.”

Rosemary Brandt
Media Relations Manager, College of Agriculture and Life Sciences