International team sequences button mushroom genomes

9 October 2012

An international collaboration of two dozen institutions led by the French National Institute for Agricultural Research (INRA) and the US Department of Energy Joint Genome Institute (DOE JGI) has fully sequenced the genes of Agaricus bisporus—the button mushroom. New work shows how its genes are actually deployed not only in leaf decay but also wood decay and in the development of fruiting bodies (the above ground part of the mushroom harvested for food).

The work also suggests how such processes have major implications for forest carbon management. The analysis of the inner workings of the world’s most cultivated mushroom was published online in the Proceedings of the National Academy of Sciences (PNAS).

Our hypothesis was that metabolic strategies and niche adaptations of Agaricus might not be present in the white-rot and brown-rot wood-decomposing fungi.

—Francis Martin, Head of the ‘ARBRE’ Lab of Excellence at INRA, Nancy, France and senior author

Compared to genomes of these fungi, that we previously characterized, the Agaricus genome surprisingly has shown many similarities in gene composition. At the same time, our data also supported the view that Agaricus fits neither brown-rot nor white-rot classifications and that its adaptation to growing in a leaf-litter humic-rich environment is not typical of classic wood degrading fungi.

—Igor Grigoriev, leader of the DOE JGI Fungal Program and senior co-author

The ancient Romans used the word “humus” to designate soil and compost, the complex natural interaction of organic compounds from plant cell wall residues. Humus contributes the chemicals that drive the decomposition process through substances like humic acid that serve as a complement to fertilizer, adding organic matter to deficient soils and contributing to overall plant health to foster root vitality and stimulate the growth of beneficial microbial communities in the soil.

Agaricus is the ideal mushroom to study for adaptation and growth in humic-rich environments, noted Grigoriev and his co-authors. They surveyed the genomes and the transcriptomes— the subset of genes expressed under particular conditions— of two A. bisporus lines, a commercial strain and related wild variety. This analysis of Agaricus turned up several families of well-known sugar-degrading enzymes similar to the repertoire found in wood-decaying fungi. However, the enzymes in Agaricus such as heme-thiolate peroxidases and etherases predominate in the presence of humus-rich soil habitats, suggesting a higher ability to metabolize complex mixtures of derivatives of lignin and other polymers.

The ability to use proteins prevalent in soil confers an advantage to Agaricus over other fungal scavengers. To our knowledge, Agaricus had not been shown in nature to decompose wood. Yet, we now see how Agaricus has adapted to growing in this ecological niche. Our understanding of the carbon cycling role of Agaricus in ecosystems is a prerequisite to modeling and optimizing carbon management for sustainable forests.

—Francis Martin

Unlike brown-rot and white-rot fungi, A. bisporus is a very poor competitor on fresh non-degraded plant wastes like wood but competes well on partially decomposed litter on forest floors and grassland soils rich in humic substrates. The comparative analysis also revealed a dozen other genes that are dialed up during mushroom formation.

“Comparative genomics of fungi just got more interesting because the contributions of Emmanuelle Morin at INRA and the 42 co-authors, many of them at the JGI, that led to analysis of the Agaricus genome. The most exciting discovery may be the expansion of these heme-thiolate peroxidases, the versatile catalysts that have an important industrial applications and seemingly allow Agaricus to live in humus, the lignin-rich residue of plants that pervade compost.

—John Taylor, Professor of Plant and Microbial Biology at the University of California, Berkeley and member of the DOE JGI Fungal Advisory Committee

Such industrial applications include the breakdown of lignin-derived compounds in novel biorefineries to obtain novel high value chemicals.

Taylor further considered the implications of the findings as applied to climate trends. “If the peroxidases do degrade humus, there could be serious effects on the sequestration of soil carbon as soil warms.”

Martin pointed out that additional value will be accrued by making the gene map of Agaricus publicly available: for identifying pathogen resistance traits and for highlighting wild germplasm collections benefiting the multi-billion dollar industry producing the button mushroom.

Resources

• Emmanuelle Morin, Annegret Kohler, Adam R. Baker, Marie Foulongne-Oriol, Vincent Lombard, Laszlo G. Nagy, Robin A. Ohm, Aleksandrina Patyshakuliyeva, Annick Brun, Andrea L. Aerts, Andrew M. Bailey, Christophe Billette, Pedro M. Coutinho, Greg Deakin, Harshavardhan Doddapaneni, Dimitrios Floudas, Jane Grimwood, Kristiina Hildén, Ursula Kües, Kurt M. LaButti, Alla Lapidus, Erika A. Lindquist, Susan M. Lucas, Claude Murat, Robert W. Riley, Asaf A. Salamov, Jeremy Schmutz, Venkataramanan Subramanian, Han A. B. Wösten, Jianping Xu, Daniel C. Eastwood, Gary D. Foster, Anton S. M. Sonnenberg, Dan Cullen, Ronald P. de Vries, Taina Lundell, David S. Hibbett, Bernard Henrissat, Kerry S. Burton, Richard W. Kerrigan, Michael P. Challen, Igor V. Grigoriev, and Francis Martin (2012) Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche PNAS doi: 10.1073/pnas.1206847109