From Competition to Cooperation - DOE Joint Genome Institute

Tracking evolution of symbiotic lifestyles across multiple fungal lineages.

The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)

The Science

By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how multiple forest fungi have independently evolved to establish symbiotic relationships with plants (mycorrhizae), and particularly how fungi that feed on decaying plant matter (saprotrophs) have transitioned to the symbiotic lifestyle.

The Impact

The analysis enables researchers to understand how plants and fungi developed symbiotic relationships, and how the mutualistic associations allow host plants, such as candidate bioenergy feedstock crops, to acquire nutrients. Additionally, these results validate how mycorrhizal fungi play an integral role in soil carbon storage.

Summary

The Russula fungal genome was among those used in the study. (Francis Martin)

There are three types of fungal saprotrophs in the forest. White rot can break down the cellulose, hemicellulose, and lignin in plant cell walls, while brown rot cannot break down the lignin but use cellulose. Finally, there are soil saprotrophs, which degrade plant detritus. Despite the different modes of nutrition, many of these soil fungi have independently evolved ectomycorrhizal (form symbiotic relationships outside of the root cells) lineages. To learn why, researchers analyzed 135 fungal genomes representing major fungal families, including those for which there were previously no genomes of symbiotic species available: 73 saprotrophs and 62 mycorrhizal species. The 62 mycorrhizal species include 29 newly-sequenced mycorrhizal genomes. With so many fungal genomes, the team conducted a large-scale comparison, charting several changes caused by the lifestyle change. For example, the number of plant cell wall-degrading enzymes such as ligninases and cellulases were much lower in ectomycorrhizal fungi compared to white rot fungi. Additionally, some of the saprotrophic genes found in the mycorrhizal species, such as nutrient transporters, were co-opted into symbiotic functions.

Recently published in Nature Communications, the work was led by a consortium of researchers from the French National Institute for Agriculture, Food and Environment (INRAE), Hungary’s Biological Research Centre, Clark University, and the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab). All of the fungal genomes used in the study are available on the JGI fungal portal MycoCosm.

The work builds upon several papers and workshops, starting with the first mycorrhizal genome sequence generated by the JGI more than a decade ago. Having these datasets will assist researchers in moving toward functional genomics studies to learn more about the inner workings of plant-host and mycorrhizal-fungal interactions.

Contacts:

BER Contact
Ramana Madupu, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
Ramana.Madupu@science.doe.gov

PI Contact
Francis Martin
Head, Lab of Excellence ARBRE
INRAE (France)
francis.martin@inrae.fr

Funding:

The project was funded by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, and supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 within the framework of the Mycorrhizal Genomics Initiative (CSP # 305), Metatranscriptomics of Forest Soil Ecosystems project (CSP # 570) and the 1000 Fungal Genome projects (CSP # 662 & 1974). This research was also supported by the Laboratory of Excellence ARBRE (ANR-11-LABX-0002-01), the Region Lorraine, the European Regional Development Fund and the Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program, the Office of Biological and Environmental Research in the US Department of Energy (DOE) Office of Science. LGN is funded by the Momentum Program of the Hungarian Academy of Sciences (Grant No. LP2019/13-2019) and the National Research, Development and Innovation office (contract No: GINOP-2.3.2-15-2016-00052). GJSz received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 714774 and the grant GINOP-2.3.2.-15-2016- 00057.

Publication:

Miyauchi S. et al. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. Nat Commun 11, 5125 (2020). doi:10.1038/s41467-020-18795-w