The mutualistic relationship between tree roots and ectomycorrhizal (ECM) fungi¹ has been shaping forest ecosystems² since their inception³. ECM fungi are key players supporting the growth, health and stress tolerance⁴ of forest trees globally, such as oak, pine, spruce, birch and beech⁵, and help boost the productivity of bioenergy feedstock trees, including poplar and willow⁶. The most common ECM fungus⁷ is Cenococcum geophilum, found in subtropical through arctic zones and especially in extreme environments. It is also the only mycorrhizal fungus in the Dothideomycetes, a large class comprised of some 19,000 fungal species, many of them plant pathogens. To learn more about what ectomycorrhizal characteristics are dominant⁸ in Cenococcum geophilum, a team led by researchers at the French National Institute for Agricultural Research (INRA) and the Swiss Federal Institute for Forest, Snow and Landscape Research WSL, and including researchers at the U.S. Department of Energy Joint⁹ Genome Institute (DOE JGI), a DOE Office of Science User Facility, compared its genome with the genomes of close relatives Lepidopterella palustris and Glonium stellatum, neither of which are ECM fungi. The study was published online September 7 in Nature Communications. They found specific adaptations in the C. geophilum transcriptome ¬- the set of its messenger RNA molecules¹⁰ that reflects actual biochemical activity by the fungus ¬-that could help their hosts be more resistant¹¹ to drought stress, a finding that could be useful in developing more plant feedstocks for bioenergy amidst the changing climate.

 

As part of a comparative genomic analysis done through the Mycorrhizal Genomics Initiative (MGI) headed by study senior author Francis Martin of INRA, the DOE JGI sequenced C. geophilum and its close relative Lepidopterella palustris, and annotated¹² both of these genomes and another close relative, Glonium stellatum. "We showed that the genome of C. geophilum, the only known mycorrhizal symbiont within the largest fungal class Dothideomycetes, acquired the same genomic adaptations to the mycorrhizal lifestyle over generations as the previously¹³ sequenced ectomycorrhizal basidiomycetes," Martin said. "These include a strikingly reduced number of plant cell wall degrading enzymes¹⁴ (PCWDEs) and a large set of symbiosis¹⁵-induced lineage-specific genes¹⁶, including dozen of mycorrhiza-induced small secreted¹⁷ effector-like proteins (MiSSPs)."Unlike free-living saprotrophs, fungi that get their nutrients¹⁸ from decomposing¹⁹ organic matter in forest soils and so require PCWDEs, Cenoccocum has come to rely heavily on its hosts for its carbon nutrition. 

 

Noting that the root tips of C. geophilum are highly resistant to dessication, one of the team's key findings is that two of the three most highly induced C. geophilum genes in symbiosis code for water channels. "The regulation of these water channel genes is fine-tuned under drought conditions and they might therefore play a key role in drought adaptation of host plants," said first author Martina Peter of the Swiss Federal Research Institute WSL.

 

"C. geophilum population genomics should shed light on the mechanisms²⁰ of host and environmental adaptation," the team wrote in their paper. "It should facilitate the identification of drought-adapted C. geophilum strains, which can be used to efficiently²¹ support their host trees threatened by the forecasted increase in drought periods in many parts of the world."

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