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1. Comparative genomics of pyrophilous fungi reveals a link between fire events and developmental genes

Author

Steindorff, Andrei S, Carver, Akiko, Calhoun, Sara, Stillman, Kyra, Liu, Haowen, Lipzen, Anna, He, Guifen, Yan, Mi, Pangilinan, Jasmyn, LaButti, Kurt, Ng, Vivian, Bruns, Thomas D, and Grigoriev, Igor V

Subjects
Fungal Proteins, Soil, Evolutionary Biology, Genes, Fungi, Developmental, Genomics, Microbiology, Carbon, Soil Microbiology, Ecosystem, Wildfires, Biotechnology
Abstract

Forest fires generate a large amount of carbon that remains resident on the site as dead and partially 'pyrolysed' (i.e. burnt) material that has long residency times and constitutes a significant pool in fire-prone ecosystems. In addition, fire-induced hydrophobic soil layers, caused by condensation of pyrolysed waxes and lipids, increase post-fire erosion and can lead to long-term productivity losses. A small set of pyrophilous fungi dominate post-fire soils and are likely to be involved with the degradation of all these compounds, yet almost nothing is currently known about what these fungi do or the metabolic processes they employ. In this study, we sequenced and analysed genomes from fungi isolated after Rim fire near Yosemite National Park in 2013 and showed the enrichment/expansion of CAZymes and families known to be involved in fruiting body initiation when compared to other basidiomycete fungi. We found gene families potentially involved in the degradation of the hydrophobic layer and pyrolysed organic matter, such as hydrophobic surface binding proteins, laccases (AA1_1), xylanases (GH10, GH11), fatty acid desaturases and tannases. Thus, pyrophilous fungi are important actors to restate the soil's functional capabilities.

Published
2021

2. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Author

Miyauchi, Shingo, Kiss, Enikő, Kuo, Alan, Drula, Elodie, Kohler, Annegret, Sánchez-García, Marisol, Morin, Emmanuelle, Andreopoulos, Bill, Barry, Kerrie W., Bonito, Gregory, Buée, Marc, Carver, Akiko, Chen, Cindy, Cichocki, Nicolas, Clum, Alicia, Culley, David, Crous, Pedro W., Fauchery, Laure, Girlanda, Mariangela, Hayes, Richard D., Kéri, Zsófia, LaButti, Kurt, Lipzen, Anna, Lombard, Vincent, Magnuson, Jon, Maillard, François, Murat, Claude, Nolan, Matt, Ohm, Robin A., Pangilinan, Jasmyn, Pereira, Maíra de Freitas, Perotto, Silvia, Peter, Martina, Pfister, Stephanie, Riley, Robert, Sitrit, Yaron, Stielow, J. Benjamin, Szöllősi, Gergely, Žifčáková, Lucia, Štursová, Martina, Spatafora, Joseph W., Tedersoo, Leho, Vaario, Lu-Min, Yamada, Akiyoshi, Yan, Mi, Wang, Pengfei, Xu, Jianping, Bruns, Tom, Baldrian, Petr, Vilgalys, Rytas, Dunand, Christophe, Henrissat, Bernard, Grigoriev, Igor V., Hibbett, David, Nagy, László G., Martin, Francis M., Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Synthetic and Systems Biology Unit [Szeged], Biological Research Centre [Szeged] (BRC), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Clark University, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Michigan State University [East Lansing], Michigan State University System, Pacific Northwest National Laboratory (PNNL), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Ben-Gurion University of the Negev (BGU), Institute of Microbiology of the Czech Academy of Sciences (MBU / CAS), Czech Academy of Sciences [Prague] (CAS), Oregon State University (OSU), Institute of Computer Science [University of Tartu, Estonie], University of Tartu, University of Helsinki, Shinshu University Hospital, McMaster University [Hamilton, Ontario], Department of Plant and Microbial Biology [Berkeley], University of California [Berkeley], University of California-University of California, Duke University [Durham], Dynamique et Evolution des Parois cellulaires végétales, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), King Abdulaziz University, Beijing Forestry University, ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), Institute of Microbiology of the Czech Academy of Sciences [Prague, Czech Republic] (MBU / CAS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Molecular Microbiology, Sub Molecular Microbiology, Department of Forest Sciences, Westerdijk Fungal Biodiversity Institute - Evolutionary Phytopathology, and Westerdijk Fungal Biodiversity Institute

Subjects
DECOMPOSITION, Chemistry(all), DATABASE, Evolution, Science, [SDV]Life Sciences [q-bio], PROTEIN, Physics and Astronomy(all), ANNOTATION, Article, MECHANISMS, Microbial ecology, Evolution, Molecular, Fungal Proteins, Mycorrhizae, Genetics, TOOL, lcsh:Science, Symbiosis, Ecosystem, Phylogeny, Plant Physiological Phenomena, Genome, ECTOMYCORRHIZAL FUNGI, Biochemistry, Genetics and Molecular Biology(all), Fungi, Molecular, Plants, NITROGEN, ALIGNMENT, Fungal, ORIGINS, 1181 Ecology, evolutionary biology, [SDE]Environmental Sciences, lcsh:Q, Evolutionary developmental biology, Genome, Fungal, Biotechnology
Abstract

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild., Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

Published
2020
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