
Bar-On YM, Phillips R, Milo R. The biomass distribution on Earth. Proc Natl Acad Sci. 2018;115:6506–11.
Batjes NH. Total carbon and nitrogen in the soils of the world. Eur J Soil Sci. 2014;65:10–21.
De Deyn GB, Cornelissen JHC, Bardgett RD. Plant functional traits and soil carbon sequestration in contrasting biomes. Ecol Lett. 2008;11:516–31.
Nielsen UN, Ayres E, Wall DH, Bardgett RD. Soil biodiversity and carbon cycling: a review and synthesis of studies examining diversity-function relationships. Eur J Soil Sci. 2011;62:105–16.
Matheny PB, Curtis JM, Hofstetter V, Aime MC, Moncalvo J-M, Ge Z-W, et al. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia. 2006;98:982–95.
Ghosh A, Frankland JC, Thurston CF, Robinson CH. Enzyme production by Mycena galopus mycelium in artificial media and in Picea sitchensis F1 horizon needle litter. Mycol Res. 2003;107:996–1008.
Steffen KT, Hofrichter M, Hatakka A. Mineralisation of 14C-labelled synthetic lignin and ligninolytic enzyme activities of litter-decomposing basidiomycetous fungi. Appl Microbiol Biotechnol. 2000;54:819–25.
Luis P, Walther G, Kellner H, Martin F, Buscot F. Diversity of laccase genes from basidiomycetes in a forest soil. Soil Biol Biochem. 2004;36:1025–36.
Barrasa JM, Blanco MN, Esteve-Raventós F, Altés A, Checa J, Martínez AT, et al. Wood and humus decay strategies by white-rot basidiomycetes correlate with two different dye decolorization and enzyme secretion patterns on agar plates. Fungal Genet Biol. 2014;72:106–14.
Liers C, Arnstadt T, Ullrich R, Hofrichter M. Patterns of lignin degradation and oxidative enzyme secretion by different wood- and litter-colonizing basidiomycetes and ascomycetes grown on beech-wood. FEMS Microbiol Ecol. 2011;78:91–102.
Lundell TK, Mäkelä MR, de Vries RP, Hildén KS Genomics, lifestyles and future prospects of wood-decay and litter-decomposing basidiomycota. In: Advances in Botanical Research. 1st ed. vol. 70. Elsevier Ltd.; 2014. p. 329–70.
Osono T. Ecology of ligninolytic fungi associated with leaf litter decomposition. Ecol Res. 2007;22:955–74.
Tanesaka E, Masuda H, Kinugawa K. Wood degrading ability of basidiomycetes that are wood decomposers, litter decomposers, or mycorrhizal symbionts. Mycologia. 1993;85:347–54.
Frankland JC, Poskitt JM, Howard DM. Spatial development of populations of a decomposer fungus, Mycena galopus. Can J Bot. 2008;73(S1):1399–406.
de Boer W, van der Wal A. Ecology of saprotrophic basidiomycetes. Br Mycol Soc Symp Ser. 2008;28:143–53.
Baldrian P, Kolaiřík M, Štursová M, Kopecký J, Valášková V, Větrovský T, et al. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J. 2012;6:248–58.
Vellinga EC. Ecology and distribution of lepiotaceous fungi (Agaricaceae)—a review. Nov Hedwig. 2004;78:273–99.
Dix NJ, Webster J. Fungal ecology. London: Chapman & Hall; 1995.
Bao D, Gong M, Zheng H, Chen M, Zhang L, Wang H, et al. Sequencing and comparative analysis of the straw mushroom (Volvariella volvacea) genome. PLoS ONE. 2013;8:e58294.
Floudas D, Held BW, Riley R, Nagy LG, Koehler G, Ransdell AS, et al. Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii. Fungal Genet Biol. 2015;76:78–92.
Albersheim P, Darvill A, Roberts K, Sederoff R, Staehelin A. Plant cell walls: from chemistry to biology. New York: Garland Science, Taylor & Francis group; 2011.
Glass NL, Schmoll M, Cate JHD, Coradetti S. Plant cell wall deconstruction by ascomycete fungi. Annu Rev Microbiol. 2013;67:477–98.
Horn SJ, Vaaje-Kolstad G, Westereng B, Eijsink VGH. Novel enzymes for the degradation of cellulose. Biotechnol Biofuels. 2012;5:45–56.
Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, et al. The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science (80-). 2012;336:1715–9.
Arantes V, Jellison J, Goodell B. Peculiarities of brown-rot fungi and biochemical Fenton reaction with regard to their potential as a model for bioprocessing biomass. Appl Microbiol Biotechnol. 2012;94:323–38.
Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, et al. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci. 2009;106:1954–9.
Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, et al. The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science (80-). 2011;333:762–5.
Kirk K, Ibach R, Mozuch MD, Conner AH, Highley TL. Characteristics of cotton cellulose depolymerized by a brown-rot fungus, by acid, or by chemical oxidants. Holzforschung. 1991;45:239–44.
Fackler K, Stevanic JS, Ters T, Hinterstoisser B, Schwanninger M, Salmén L. Localisation and characterisation of incipient brown-rot decay within spruce wood cell walls using FT-IR imaging microscopy. Enzym Micro Technol. 2010;47:257–67.
Howell C, Steenkjær Hastrup AC, Goodell B, Jellison J. Temporal changes in wood crystalline cellulose during degradation by brown rot fungi. Int Biodeterior Biodegrad. 2009;63:414–9.
Goodell B, Zhu Y, Daniel G, Groom L, Yoshida M, Kafle K, et al. Modification of the nanostructure of lignocellulose cell walls via a non-enzymatic lignocellulose deconstruction system in brown rot wood-decay fungi. Biotechnol Biofuels. 2017;10:1–15.
Nagy LG, Riley R, Tritt A, Adam C, Daum C, Floudas D, et al. Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities. Mol Biol Evol. 2016;33:959–70.
Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, et al. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet. 2015;47:410–5.
Sipos G, Prasanna AN, Walter MC, O’Connor E, Bálint B, Krizsán K, et al. Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria. Nat Ecol Evol. 2017;1:1931–41.
Almási É, Sahu N, Krizsán K, Bálint B, Kovács GM, Kiss B, et al. Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae. New Phytol. 2019;224:902–915.
Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, et al. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci. 2014;111:9923–8.
Binder M, Justo A, Riley R, Salamov A, Lopez-Giraldez F, Sjökvist E, et al. Phylogenetic and phylogenomic overview of the Polyporales. Mycologia. 2013;105:1350–73.
Ohm RA, De Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, et al. Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol. 2010;28:957–63.
Stajich JE, Wilke SK, Ahren D, Au CH, Birren BW, Borodovsky M, et al. Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci. 2010;107:11889–94.
Fernandez-Fueyo E, Ruiz-Dueñas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, et al. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc Natl Acad Sci USA. 2012;109:5458–63.
Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, Nagy LG, et al. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Natl Acad Sci. 2012;109:17501–6.
Zugmaier W, Oberwinkler F. Tremelloid haustorial cells with haustorial filaments and potential host range of Tremella mesenterica. Nord J Bot. 1995;15:207–13.
Seifert KA. Decay of wood by the dacrymycetales. Mycologia. 1983;75:1011–1018.
Ginns J, Lefebvre MNL Lignicolous Corticiod Funbgi (Basidiomycota) of North America. Systematics, Distribution, and Ecology. Mycol Mem. 1993;19:28–9.
Nakasone K. Cultural studies and identification of wood-inhabiting Corticiaceae and selected Hymenomycetes from North America. Mycol Mem. 1990;15:1–412.
Jarosch M, Besl H. Leucogyrophana, a polyphyletic genus of the order Boletales (Basidiomycetes). Plant Biol. 2001;3:443–8.
Gilbertson RL, Ryvarden L. North American polypores. Vol. 1. Abortiporus–Lindtneria. (Fungiflora A/S, Oslo, 1986).
Ginns J, Gilbertson RL, Ryvarden L. North American Polypores, Vol. 2, Megasporoporia–Wrightoporia. (Fungiflora A/S, Oslo, 1987).
Knudsen H, Vesterholt J. Key to genera, electronic keys to species. Funga Nordica: Agaricoid, Boletoid, Clavarioid, Cyphelloid and Gastroid Genera; 2008.
Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30:1236–40.
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019;47(D1):D427–32.
Peng M, Aguilar-Pontes MV, Hainaut M, Henrissat B, Hildén K, Mäkelä MR, et al. Comparative analysis of basidiomycete transcriptomes reveals a core set of expressed genes encoding plant biomass degrading enzymes. Fungal Genet Biol. 2018;112:40–6.
Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, et al. Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinforma. 2011;Suppl 35):1–19.
Jiao C, Xiong J. Accessibility and morphology of cellulose fibres treated with sodium hydroxide. BioResources. 2014;9:6504–13.
Felten J, Hall H, Jaumot J, Tauler R, De Juan A, Gorzsás A. Vibrational spectroscopic image analysis of biological material using multivariate curve resolution-alternating least squares (MCR-ALS). Nat Protoc. 2015;10:217–40.
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42(D1):490–5.
Hofrichter M, Ullrich R, Pecyna MJ, Liers C, Lundell T. New and classic families of secreted fungal heme peroxidases. Appl Microbiol Biotechnol. 2010;87:871–97.
Sprockett DD, Piontkivska H, Blackwood CB. Evolutionary analysis of glycosyl hydrolase family 28 (GH28) suggests lineage-specific expansions in necrotrophic fungal pathogens. Gene. 2011;479:29–36.
Budtova T, Navard P. Cellulose in NaOH–water based solvents: a review. Cellulose. 2016;23:5–55.
Fischer S, Schenzel K, Fischer K, Diepenbrock W. Applications of FT Raman spectroscopy and micro spectroscopy characterizing cellulose and cellulosic biomaterials. Macromol Symp. 2005;223:41–56.
Schenzel K, Fischer S. NIR FT Raman spectroscopy—a rapid analytical tool for detecting the transformation of cellulose polymorphs. Cellulose. 2001;8:49–57.
Schenzel K, Fischer S. Applications of Ft raman spectroscopy for the characterization of cellulose. Lenzing Ber. 2004;83:64–70.
Schenzel K, Fischer S, Brendler E. New method for determining the degree of cellulose I crystallinity by means of FT Raman spectroscopy. Cellulose. 2005;12:223–31.
Szymańska-Chargot M, Cybulska J, Zdunek A. Sensing the structural differences in cellulose from apple and bacterial cell wall materials by Raman and FT-IR Spectroscopy. Sensors. 2011;11:5543–60.
Igarashi K, Koivula A, Wada M, Kimura S, Penttilä M, Samejima M. High speed atomic force microscopy visualizes processive movement of Trichoderma reesei cellobiohydrolase I on crystalline cellulose. J Biol Chem. 2009;284:36186–90.
Vanden WymelenbergA, Gaskell J, Mozuch M, Sabat G, Ralph J, Skyba O, et al. Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium. Appl Environ Microbiol. 2010;76:3599–610.
Suzuki H, MacDonald J, Syed K, Salamov A, Hori C, Aerts A, et al. Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. BMC Genomics. 2012;13:1.
Yoshida M, Sato K, Kaneko S, Fukuda K. Cloning and Transcript Analysis of Multiple Genes Encoding the Glycoside Hydrolase Family 6 Enzyme from Coprinopsis cinerea. Biosci Biotechnol Biochem. 2009;73:67–73.
Theuerl S, Dörr N, Guggenberger G, Langer U, Kaiser K, Lamersdorf N, et al. Response of recalcitrant soil substances to reduced N deposition in a spruce forest soil: Integrating laccase-encoding genes and lignin decomposition. FEMS Microbiol Ecol. 2010;73:166–77.
Moreira LRS, Filho EXF. Insights into the mechanism of enzymatic hydrolysis of xylan. Appl Microbiol Biotechnol. 2016;100:5205–14.
Presley GN, Panisko E, Purvine SO, Schilling JS. Coupling secretomics with enzyme activities to compare the temporal processes of wood metabolism among white and brown rot fungi. Appl Environ Microbiol. 2018;84:e00159–18.
Lefebvre MNL. Lignicolous corticioid fungi (Basidiomycota) of North America: systematics, distri bution and ecology. Mycol Mem. 1993;19:1–247.
Ayuso-Fernández I, Ruiz-Dueñas FJ, Martínez AT. Evolutionary convergence in lignin-degrading enzymes. Proc Natl Acad Sci. 2018;115:6428–33.
Ayuso-Fernández I, Rencoret J, Gutiérrez A, Ruiz-Dueñas FJ, Martínez AT. Peroxidase evolution in white-rot fungi follows wood lignin evolution in plants. Proc Natl Acad Sci. 2019;116:17900–5.
Eichlerová I, Homolka L, Žifčáková L, Lisá L, Dobiášová P, Baldrian P. Enzymatic systems involved in decomposition reflects the ecology and taxonomy of saprotrophic fungi. Fungal Ecol. 2015;13:10–22.
Arantes V, Goodell B. Current understanding of brown-rot fungal biodegradation mechanisms: a review. In: Deterioration and Protection of Sustainable Biomaterials. ACS Symposium Series. vol. 1158. American Chemical Society; 2014. p. 1–3.
Wu M, Beckham GT, Larsson AM, Ishida T, Kim S, Payne CM, et al. Crystal structure and computational characterization of the lytic polysaccharide monooxygenase GH61D from the basidiomycota fungus Phanerochaete chrysosporium. J Biol Chem. 2013;288:12828–39.
Nimlos MR, Beckham GT, Matthews JF, Bu L, Himmel ME, Crowley MF. Binding preferences, surface attachment, diffusivity, and orientation of a family 1 carbohydrate-binding module on cellulose. J Biol Chem. 2012;287:20603–12.
Beckham GT, Matthews JF, Bomble YJ, Bu L, Adney WS, Himmel ME, et al. Identification of amino acids responsible for processivity in a family 1 carbohydrate-binding module from a fungal cellulase. J Phys Chem B. 2010;114:1447–53.
Igarashi K, Takayuki U, Anu K, Masahisa W, Satoshi K, Tetsuaki O, et al. Traffic jams reduce hydrolytic efficiency of cellulase on cellulose surface. Science (80-). 2011;333:1279–82.
Varga T, Krizsán K, Földi C, Dima B, Sánchez-García M, Sánchez-Ramírez S, et al. Megaphylogeny resolves global patterns of mushroom evolution. Nat Ecol Evol. 2019;3:668–78.
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