Current Research

The overall research goal is to elucidate the mechanisms that wood- and soil-inhabiting fungi use to break down woody biomass. Key chemical changes that the fungi cause in lignin and cellulose are identified by nuclear magnetic resonance spectroscopic analyses of natural abundance and isotope-enriched substrates, as well as by other spectroscopic techniques. Fungal enzymes and metabolites that reproduce these reactions in the test tube are then sought, using gene sequence analyses, purification of the most interesting encoded enzymes, and isolation of enzyme substrates that the fungi secrete. The results are being used to assist in the design of new biomass-modifying cocktails that may be useful in paper manufacture and biofuels production from forest residues.

Research Interests

• New solution-state NMR approach for elucidation of fungal and enzyme/mediator delignification systems
• Mechanism and physiological role of peroxygenases from litter-decomposing fungi
• Metabolomic analysis of lignocellulose colonized by white rot fungi
• Heterologous expression and functional analysis of lignocellulose-degrading enzymes from wood decay fungi.

Featured Publications & Products

• Kinne, Matthias; Zeisig, Christian; Ullrich, Rene; Kayser, Gernot; Hammel, Kenneth E.; Hofrichter, Martin. 2010. Stepwise oxygenations of toluene and 4-nitrotoluene by a fungal peroxygenase.
• Kapich, Alexander N.; Korneichik, Tatyana V.; Hatakka, Annele; Hammel, Kenneth E. 2010. Oxidizability of unsaturated fatty acids and of a non-phenolic lignin structure in the manganese peroxidase-dependent lipid peroxidation system.
• Wei, Dongsheng; Houtman, Carl J.; Kapich, Alexander N.; Hunt, Christopher G.; Cullen, Daniel; Hammel, Kenneth E. 2010. Laccase and its role in production of extracellular reactive oxygen species during wood decay by the brown rot basidiomycete Postia placenta.
• Kinne, Matthias; Poraj-Kobielska, Marzena; Aranda, Elisabet; Ullrich, Rene; Hammel, Kenneth E.; Scheibner, Katrin; Hofrichter, Martin. 2009. Regioselective preparation of 5-hydroxypropranolol and 4 -hydroxydiclofenac with a fungal peroxygenase.
• Kinne, Matthias; Poraj-Kobielska, Marzena; Ralph, Sally A.; Ullrich, Rene; Hofrichter, Martin; Hammel, Kenneth E. 2009. Oxidative cleavage of diverse ethers by an extracellular fungal peroxygenase.

Publications

• Houtman, Carl J.; Maligaspe, Eranda ; Hunt, Christopher G.; Fernández-Fueyo, Elena ; Martínez, Angel T.; Hammel, Kenneth E. 2018. Fungal lignin peroxidase does not produce the veratryl alcohol cation radical as a diffusible ligninolytic oxidant.
• Hall, Steven J.; Huang, Wenjuan; Hammel, Kenneth. 2017. An optical method for carbon dioxide isotopes and mole fractions in small gas samples: tracing microbial respiration from soil, litter, and lignin..
• Hunt, Christopher G.; Lacher, Steven; Hirth, Kolby; Lorenz, Linda; Hammel, Kenneth E. 2017. Exploring the hypothesis that limiting diffusion of fungal oxidants underlies decay resistance in acetylated wood.
• Houtman, Carl J.; Kitin, Peter; Houtman, Jon C. D.; Hammel, Kenneth E.; Hunt, Christopher G. 2016. Acridine Orange Indicates Early Oxidation of Wood Cell Walls by Fungi.
• Im, Chak Han; Park, Young-Hoon; Hammel, Kenneth E.; Park, Bokyung; Kwon, Soon Wook; Ryu, Hojin; Ryu, Jae-San. 2016. Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii.
• Hall, Steven J.; Silver, Whendee L.; Timokhin, Vitaliy I.; Hammel, Kenneth E. 2016. Iron addition to soil specifically stabilized lignin.
• Zhang, Jiwei; Presley, Gerald N.; Hammel, Kenneth E.; Ryu, Jae-San; Menke, Jon R.; Figueroa, Melania; Hu, Dehong; Orr, Galya; Schilling, Jonathan S. 2016. Localizing gene regulation reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta.
• Linde, Dolores; Ruiz-Dueñas, Francisco J.; Fernández-Fueyo, Elena; Guallar, Victor; Hammel, Kenneth E.; Pogni, Rebecca; Martínez, Angel T. 2015. Basidiomycete DyPs: Genomic diversity, structural-functional aspects, reaction mechanism and environmental significance.
• Hall, Steven J.; Silver, Whendee L.; Timokhin, Vitaliy I.; Hammel, Kenneth E. 2015. Lignin decomposition is sustained under fluctuating redox conditions in humid tropical forest soils.
• Korripally, Premsagar; Hunt, Christopher G.; Houtman, Carl J.; Jones, Don C.; Kitin, Peter J.; Cullen, Dan; Hammel, Kenneth E.; Brakhage, A. A. 2015. Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood.
• Yelle, Daniel J.; Kapich, Alexander N.; Houtman, Carl J.; Lu, Fachuang; Timokhin, Vitaliy I.; Fort Jr., Raymond C.; Ralph, John; Hammel, Kenneth E. 2014. A Highly Diastereoselective Oxidant Contributes to Ligninolysis by the White Rot Basidiomycete Ceriporiopsis subvermispora.
• Fernández-Fueyo, Elena; Ruiz-Dueñas, Francisco J; Martinez, María Jesús; Romero, Antonio; Hammel, Kenneth E; Medrano, Francisco Javier; Martínez, Angel T. 2014. Ligninolytic peroxidase genes in the oyster mushroom genome: heterologous expression, molecular structure, catalytic and stability properties, and lignin-degrading ability.
• Korripally, Premsagar; Timokhin, Vitaliy I.; Houtman, Carl J.; Mozuch, Michael D.; Hammel, Kenneth E. 2013. Evidence from Serpula lacrymans that 2,5-Dimethoxyhydroquinone Is a Lignocellulolytic Agent of Divergent Brown Rot Basidiomycetes.
• Miki, Yuta; Pogni, Rebecca; Acebes, Sandra; Lucas, Fatima; Fernandez-Fueyo, Elena; Baratto, Maria Camilla; Fernandez, Maria I.; Rios, Vivian De Los; Ruiz-duenas, Francisco J.; Sinicropi, Adalgisa; Basosi, Riccardo; Hammel, Kenneth E.; Guallar, Victor; Martinez, Angel T. 2013. Formation of a tyrosine adduct involved in lignin degradation by Trametopsis cervina lignin peroxidase: a novel peroxidase activation mechanism.
• Hunt, Christopher G.; Houtman, Carl J.; Jones, Don C.; Kitin, Peter; Korripally, Premsagar; Hammel, Kenneth E. 2013. Spatial mapping of extracellular oxidant production by a white rot basidiomycete on wood reveals details of ligninolytic mechanism.
• Fernandez-Fueyo, Elena; Ruiz-Dueñas, Francisco J.; Ferreira, Patricia; Floudas, Dimitrios; Hibbett, David S.; Canessa, Paulo; Larrondo, Luis F.; James, Tim Y.; Seelenfreund, Daniela; Lobos, Sergio; Polanco, Rubén; Tello, Mario; Honda, Yoichi; Watanabe, Takahito; Watanabe, Takashi; Ryu, Jae San; Kubicek, Christian P.; Schmoll, Monika; Gaskell, Jill; Hammel, Kenneth E.; St. John, Franz J.; Wymelenberg, Amber Vanden; Sabat, Grzegorz; BonDurant, Sandra Splinter; Syed, Khajamohiddin; Yadav, Jagjit S.; Dodapaneni, Harshavardhan; Subramanian, Venkataramanan; Lavin, José L.; Oguiza, José A.; Perez, Gumer; Pisabarro, Antonio G.; Ramirez, Lucia; Santoyo, Francisco; Master, Emma; Coutinho, Pedro M.; Henrissat, Bernard; Lombard, Vincent; Magnuson, Jon Karl; Kües, Ursula; Hori, Chiaki; Igarashi, Kiyohiko; Samejima, Masahiro; Held, Benjamin W.; Barry, Kerrie W.; LaButti, Kurt M.; Lapidus, Alla; Lindquist, Erika A.; Lucas, Susan M.; Riley, Robert; Salamov, Asaf A.; Hoffmeister, Dirk; Schwenk, Daniel; Hadar, Yitzhak; Yarden, Oded; de Vries, Ronald P.; Wiebenga, Ad; Stenlid, Jan; Eastwood, Daniel; Grigoriev, Igor V.; Berka, Randy M.; Blanchette, Robert A.; Kersten, Phil; Martinez, Angel T.; Vicuna, Rafael; Cullen, Daniel. 2012. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.
• Fernandez-Fueyo, Elena; Ruiz-Duenas, Francisco J.; Miki, Yuta; Martinez, Marta Jesus; Hammel, Kenneth E.; Martinez, Angel T. 2012. Lignin-degrading Peroxidases from Genome of Selective Ligninolytic Fungus Ceriporiopsis subverispora.
• Kapich, Alexander N.; Korneichik, Tatyana V.; Hammel, Kenneth E.; Hatakka, Annele. 2011. Comparative evaluation of manganese peroxidase- and Mn(III)-initiated peroxidation of C18 unsaturated fatty acids by different methods.
• Langan, Paul; Gnankaran, S.; Rector, Kirk D.; Pawley, Norma; Fox, David T.; Cho, Dae Won; Hammel, Kenneth E. 2011. Exploring new strategies for cellulosic biofuels production.
• Yelle, Daniel J.; Wei, Dongsheng; Ralph, John; Hammel, Kenneth E. 2011. Multidimensional NMR analysis reveals truncated lignin structures in wood decayed by the brown rot basidiomycete Postia placenta.
• Kinne, Matthias; Poraj-Kobielska, Marzena; Ullrich, Rene; Nousiainen, Paula; Sipilä, Jussi; Scheibner, Katrin; Hammel, Kenneth E.; Hofrichter, Martin. 2011. Oxidative cleavage of non-phenolic β-O-4 lignin model dimers by an extracellular aromatic peroxygenase.
• Poraj-Kobielska, Marzena; Kinne, Matthias; Ullrich, René; Scheibner, Katrin; Kayser, Gernot; Hammel, Kenneth E.; Hofrichter, Martin. 2011. Preparation of human drug metabolites using fungal peroxygenases.
• Ryu, Jae San; Shary, Semarjit; Houtman, Carl J.; Panisko, Ellen A.; Korripally, Premsagar; St. John, Franz J.; Crooks, Casey; Siika-aho, Matti; Magnuson, Jon K.; Hammel, Kenneth E. 2011. Proteomic and functional analysis of the cellulase system expressed by Postia placenta during brown rot of solid wood.
• Hatakka, Annele; Hammel, Kenneth E. 2010. Fungal biodegradation of lignocelluloses.
• Martinez, Diego; Challacombe, Jean; Morgenstern, Ingo; Hibbett, David; Schmoll, Monika; Kubicek, Christian P.; Ferreira, Patricia; Ruiz-Duenas, Francisco J.; Martinez, Angel T.; Kersten, Philip J.; Hammel, Kenneth E.; Gaskell, Jill A.; Cullen, Daniel. 2009. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion.
• Ralph, John; Lu, Fachuang; Kim, Hoon; Ress, Dino; Yelle, Daniel J.; Hammel, Kenneth E.; Ralph, Sally A.; Nanayakkara, Bernadette; Wagner, Armin; Akiyama, Takuya; Schatz, Paul F.; Mansfield, Shawn D.; Terashima, Noritsugu; Boerjan, Wout; Sundberg, Bjorn; Hedenstrom, Mattias. 2009. High-resolution solution-state NMR of unfractionated plant cell walls.
• Shary, Semarjit; Kapich, Alexander N.; Panisko, Ellen A.; Magnuson, Jon K.; Cullen, Daniel; Hammel, Kenneth E. 2008. Differential expression in Phanerochaete chrysosporium of membrane- associated proteins relevant to lignin degradation.
• Yelle, Daniel J.; Ralph, John; Lu, Fachuang; Hammel, Kenneth E. 2008. Evidence for cleavage of lignin by a brown rot basidiomycete.
• Kinne, Matthias; Ullrich, Rene; Hammel, Kenneth E.; Scheibner, Katrin; Hofrichter, Martin. 2008. Regioselective preparation of (R)-2-(4-hydroxyphenoxy)propionic acid with a fungal peroxygenase.
• Hammel, Kenneth E.; Cullen, Dan. 2008. Role of fungal peroxidases in biological ligninolysis.
• Ortiz-Bermudez, Patricia; Hirth, Kolby C.; Srebotnik, Ewald; Hammel, Kenneth E. 2007. Chlorination of lignin by ubiquitous fungi has a likely role in global organochlorine production.
• Shary, Semarjit; Ralph, Sally A.; Hammel, Kenneth E. 2007. New insights into the ligninolytic capability of a wood decay ascomycete.
• Suzuki, Melissa R.; Hunt, Christopher G.; Houtman, Carl J.; Dalebroux, Zachary D.; Hammel, Kenneth E. 2006. Fungal hydroquinones contribute to brown rot of wood.
• Cohen, Roni; Suzuki, Melissa R.; Hammel, Kenneth E. 2005. Processive endoglucanase active in crystalline cellulose hydrolysis by the brown rot Basidiomycete Gloeophyllum trabeum.
• Cohen, Roni; Suzuki, Melissa R.; Hammel, Kenneth E. 2004. Differential stress-induced regulation of two quinone reductases in the brown rot Basidiomycete Gloeophyllum trabeum.
• Ortiz-Bermudez, Patricia; Srebotnik, Ewald; Hammel, Kenneth E. 2003. Chlorination and cleavage of lignin structures by fungal chloroperoxidases.
• Cohen, Roni; Jensen, Kenneth A.; Houtman, Carl J.; Hammel, Kenneth E. 2002. Significant levels of extracellular reactive oxygen species produced by brown rot basidiomycetes on cellulose.
• Kapich, Alexander N.; Jensen, Kenneth A.; Hammel, Kenneth E. 1999. Peroxyl radicals are potential agents of lignin biodegradation.

Research Highlights

Highlight	Title	Year
FPL-2015-200	How Does Wood Decay Start? How do fungi rot wood? Using new tools, fluorescent dye attached to tiny beads, and laser confocal microscopy, Forest Service scientists were ab ...	2015
FPL-2010-028	Water, Air, and Soil Forest fungi perform an essential role in recycling woody plant debris and have many potential applications in biotechnology. In 2009, a Forest ...	2010