Progress 10/01/12 to 09/30/22
Outputs
OUTPUTS: Wood and litter degrading fungi are essential components of forest carbon cycling. The enzymatic mechanisms they employ are poorly understood but offer unparalleled opportunities for the development of industrial processes. Two basic categories of decay fungi have long been recognized; white rot and brown rot. All components of plant cell walls, including the highly recalcitrant lignin, are efficiently mineralized during white rot. Oxidative degradation of lignin is thought to involve extracellular peroxidases coupled to peroxide-generating oxidases. The white rot fungi also progressively deconstruct cellulose and hemicellulose using an array of glycoside hydrolases. In contrast, bulk lignin remains as a polymeric residue during brown rot, while cellulose is rapidly depolymerized. Resilient brown rot residues contribute to the carbon pool in humic soils, particularly in boreal, conifer-dominated ecosystems. Uncertainty about the mechanisms of lignocellulose degradation has been an obstacle to understanding microbial interactions in forest soils and to the development of commercial processes dependent on bioconversions. Addressing the issue, collaborative efforts with the U.S. Department of Energy and universities have characterized the entire genome of several wood decay fungi. These genomes have reveal impressive sequence diversity, and recent functional analyses are providing a deeper understanding of plant cell wall deconstruction and the transformation of organopollutants. Hundreds of enzymes involved, directly or indirectly, in the conversion of recalcitrant lignocellulose to high value products. These studies showed that substrate composition substantially altered gene expression suggesting that commercial enzyme mixtures could be tailored to specific woody substrates. Beyond this, newly available genome resources have substantially enhanced our knowledge of mechanisms of lignocellulose conversions and revealed new and novel enzymes with considerable potential in emerging technologies. Thus, the findings facilitate development of enzymatic systems for the efficient conversion of an expanding number of forest feedstocks. PARTICIPANTS: Aix Marseille University, U.S. Department of Energy, Univerisite de Lorraine, Utrecht University, Leiden University, University of Helsinki, Georg-August University Gottingen, Centro de Investigaciones Biologicas Madrid, University of Wisconsin Biotechnology Center. TARGET AUDIENCES: Intended audiences are from academia and industry. PROJECT MODIFICATIONS: The problem area will be continuing with into the new problem 4C beginning FY21.
Impacts
Our FY2020 research identified specific enzymes key to the degradation of lignin, the recalcitrant polymer that interferes with efficient deconstruction and utilization of lignocellulosic biomass. In one case, a large international group of cooperators examined the substrait specificity of several species of the lignin-degrading fungi within Pycnoporus. In a separate study, the ligninolytic enzymes secreted by Phlebiopsis gigantea were systematically and unambiguously identified by mass spectrometry.
Publications
- Miyauchi, Shingo; Hage, Hayat; Drula, Elodie; Lesage-Meessen, Laurence; Berrin, Jean-Guy; Navarro, David; Favel, Anne; Chaduli, Delphine; Grisel, Sacha; Haon, Mireille; Piumi, François; Levasseur, Anthony; Lomascolo, Anne; Ahrendt, Steven; Barry, Kerrie; LaButti, Kurt M; Chevret, Didier; Daum, Chris; Mariette, Jérôme; Klopp, Christophe; Cullen, Daniel; de Vries, Ronald P; Gathman, Allen C; Hainaut, Matthieu; Henrissat, Bernard; Hildén, Kristiina S; Kües, Ursula; Lilly, Walt; Lipzen, Anna; Mäkelä, Miia R; Martinez, Angel T; Morel-Rouhier, Mélanie; Morin, Emmanuelle; Pangilinan, Jasmyn; Ram, Arthur F J; Wösten, Han A B; Ruiz-Dueñas, Francisco J; Riley, Robert; Record, Eric; Grigoriev, Igor V; Rosso, Marie-Noëlle. 2020. Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus. DNA Research. 27(2). 14 p.
- Sabat, G.; Cullen, D. 2020. Mechanism of extractive degradation by Phlebiopsis gigantea. Protiome xchange dataset. Accession number PXD021332. Hinxton, Cambridge, UK: EMBL-EBI.
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Progress 10/01/12 to 09/30/19
Outputs
OUTPUTS: Wood and litter degrading fungi are essential components of forest carbon cycling. The enzymatic mechanisms they employ are poorly understood but two basic categories of decay fungi are recognized; white rot and brown rot. All components of plant cell walls are efficiently mineralized by white rot fungi. In particular, the cell wall polymer lignin is degraded, along with the wood carbohydrates. Oxidative degradation of lignin is thought to involve extracellular peroxidases coupled to peroxide-generating oxidases. The white rot fungi also progressively deconstruct cellulose and hemicellulose using an array of glycoside hydrolases. In contrast, bulk lignin remains as a polymeric residue of decay by brown rot fungi, while cellulose is rapidly depolymerized. Resilient brown rot residues contribute to the carbon pool in humic soils. Uncertainty about the mechanisms of lignocellulose degradation has been an obstacle to understanding microbial interactions in forest soils and to the development of commercial processes dependent on bioconversions. Addressing the issue, collaborative efforts with the US Department of Energy and universities have characterized the entire genome of several wood decay fungi. The annotated sequence provides a useful community resource that greatly simplifies and clarifies research on brown rot fungi.
Impacts
Our bioinformatics strategies are broadly applicable to the rapidly increasing number of available genomes and thereby facilitate the identification of enzymes key to the degradation of lignin, a recalcitrant polymer that interferes with efficient deconstruction and utilization of lignocellulosic biomass.
Publications
- Bhatnagar, Jennifer M.; Sabat, Grzegorz; Cullen, Daniel. 2019. The foliar endophyte Phialocephala scopiformis DAOMC 229536 proteome when grown on wood used as the sole carbon source. Microbiology Resource Announcements. 8(6). 3 p.
- Wu, Baojun; Gaskell, Jill; Zhang, Jiwei; Toapanta, Christina; Ahrendt, Steven; Grigoriev, Igor V.; Blanchette, Robert A.; Schilling, Jonathan S.; Master, Emma; Cullen, Daniel; Hibbett, David S. 2019. Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi. The ISME Journal. 13(6): 1391-1403.
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Progress 10/01/17 to 09/30/18
Outputs
OUTPUTS: Wood and litter degrading fungi are essential components of forest carbon cycling. The enzymatic mechanisms they employ are poorly understood but two basic categories of decay fungi are recognized; white rot and brown rot. All components of plant cell walls are efficiently mineralized by white rot fungi. In particular, the cell wall polymer lignin is degraded, along with the wood carbohydrates. Oxidative degradation of lignin is thought to involve extracellular peroxidases coupled to peroxide-generating oxidases. The white rot fungi also progressively deconstruct cellulose and hemicellulose using an array of glycoside hydrolases. In contrast, bulk lignin remains as a polymeric residue of decay by brown rot fungi, while cellulose is rapidly depolymerized. Resilient brown rot residues contribute to the carbon pool in humic soils. Uncertainty about the mechanisms of lignocellulose degradation has been an obstacle to understanding microbial interactions in forest soils and to the development of commercial processes dependent on bioconversions. Addressing the issue, collaborative efforts with the US Department of Energy and universities have characterized the entire genome of several wood decay fungi. The annotated sequence provides a useful community resource that greatly simplifies and clarifies research on brown rot fungi. Resent research has focused on the variety lignin degrading enzymes that were found on a sample of decaying Pinus contorta (Lodgepole Pine) and gene expression by the brown rot fungus Fomitopsis pinicola
Impacts
Our bioinformatics strategies are broadly applicable to the rapidly increasing number of available genomes and thereby facilitate the identification of enzymes key to the degradation of lignin, a recalcitrant polymer that interferes with efficient deconstruction and utilization of lignocellulosic biomass.
Publications
- Hori, Chiaki; Gaskell, Jill; Cullen, Dan; Sabat, Grzegorz; Stewart, Philip E.; Lail, Kathleen; Peng, Yi; Barry, Kerrie; Grigoriev, Igor V.; Kohler, Annegret; Fauchery, Laure; Martin, Francis; Zeiner, Carolyn A.; Bhatnagar, Jennifer M. 2018. Multi-omic analyses of extensively decayed Pinus contorta reveal expression of a diverse array of lignocellulose-degrading enzymes. Applied and Environmental Microbiology. 84(20): 1-41.
- Wu, Baojun; Gaskell, Jill; Held, Benjamin W.; Toapanta, Cristina; Vuong, Thu; Ahrendt, Steven; Lipzen, Anna; Zhang, Jiwei; Schilling, Jonathan S.; Master, Emma; Grigoriev, Igor V.; Blanchette, Robert A.; Cullen, Dan; Hibbett, David S. 2018. Substrate-specific differential gene expression and RNA editing in the brown rot fungus Fomitopsis pinicola . Applied and Environmental Microbiology. 84(16): 1-19.
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Progress 10/01/12 to 09/30/17
Outputs
OUTPUTS: Wood and litter degrading fungi are essential components of forest carbon cycling. The enzymatic mechanisms they employ are poorly understood but two basic categories of decay fungi are recognized; white rot and brown rot. All components of plant cell walls, including the highly recalcitrant lignin, are efficiently mineralized during white rot. Oxidative degradation of lignin is thought to involve extracellular peroxidases coupled to peroxide-generating oxidases. The white rot fungi also progressively deconstruct cellulose and hemicellulose using an array of glycoside hydrolases. In contrast, bulk lignin remains as a polymeric residue during brown rot, while cellulose is rapidly depolymerized. Substantial evidence has supported the involvement of low molecular weight, diffusible oxidants such as hydroxyl radical. Resilient brown rot residues contribute to the carbon pool in humic soils, particularly in boreal, conifer-dominated ecosystems. Uncertainty about the mechanisms of lignocellulose degradation has been an obstacle to understanding microbial interactions in forest soils and to the development of commercial processes dependent on bioconversions. Addressing the issue, collaborative efforts with the US Department of Energy and universities have characterized the entire genome of several wood decay fungi. Among the brown rot fungi, we published the genome sequence of a model Postia placenta strain during FY17. The annotated sequence provides a useful community resource that greatly simplifies and clarifies research on brown rot fungi. Nevertheless, deriving evolutionary relationships and understanding physiological processes based on such genomes remains a daunting challenge. Addressing this issue, a bioinformatics strategy has been developed by an international team of academic and government labs. Published in a high-impact, peer reviewed journal, large-scale genome comparisons were verified by experimentally determined transcriptomes. The approach allows inferences regarding the role of hundreds of genes, many of which were hitherto completely unknown. Thus, the method opens whole new paths of research and development related to lignocellulose bioconversions. Beyond these laboratory studies, we substantially increased research on the role of wood decay fungi in forest restoration following catastrophic wildfire in Western lodgepole pine forests. In collaboration with the DoE⿿s Joint Genome Institute and the University of Wisconsin, our ⿿omic⿿ investigations have defined microbial communities in soil, litter and wood samples. Brown and white rot fungi were particularly abundant and direct protein sequencing unambiguously identified thousands of enzymes, all of which have been made publicly accessible. Overall, these investigations revealed a remarkable diversity of novel enzymes with considerable potential in emerging technologies. Moreover, the data contribute to our understanding of microbial communities and physiological processes succeeding Western wildfires. PARTICIPANTS: During FY2017, significant participants included the US Department Energy Joint Genome Institute, Clark University, the University of Minnesota, Hokkaido University and Boston University. TARGET AUDIENCES: Academia and industry.
Impacts
Our bioinformatics strategies are broadly applicable to the rapidly increasing number of available genomes and thereby facilitate the identification of enzymes key to the degradation of lignin, a recalcitrant polymer that interferes with efficient deconstruction and utilization of lignocellulosic biomass. In addition, our published Postia placenta genome will accelerate research and contribute to our understanding of cellulose depolymerization. Finally, our microbiome studies of fire disturbed Western forests provide unparalleled insight into microbial communities. The structure and physiological activities within these communities are central to carbon cycling, and the enzymes discovered may aid bioprocess development.
Publications
- Gaskell, Jill; Kersten, Phil; Larrondo, Luis F.; Canessa, Paulo; Martinez, Diego; Hibbett, David; Schmoll, Monika; Kubicek, Christian P.; Martinez, Angel T.; Yadav, Jagjit; Master, Emma; Magnuson, Jon Karl; Yaver, Debbie; Berka, Randy; Lail, Kathleen; Chen, Cindy; LaButti, Kurt; Nolan, Matt; Lipzen, Anna; Aerts, Andrea; Riley, Robert; Barry, Kerrie; Henrissat, Bernard; Blanchette, Robert; Grigoriev, Igor V.; Cullen, Dan. 2017. Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12. Genomics Data. 14: 21-23.
- Nagy, László G.; Riley, Robert; Bergmann, Philip J.; Krizsán, Krisztina; Martin, Francis M.; Grigoriev, Igor V.; Cullen, Dan; Hibbett, David S. 2016. Genetic bases of fungal white rot wood decay predicted by phylogenomic analysis of correlated gene-phenotype evolution. Molecular Biology and Evolution. 34(1): 35-44.
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Progress 10/01/15 to 09/30/16
Outputs
OUTPUTS: Wood and litter degrading fungi are essential components of forest carbon cycling. The enzymatic mechanisms they employ are poorly understood but offer unparalleled opportunities for the development of industrial processes. Two basic categories of decay fungi have long been recognized; white rot and brown rot. All components of plant cell walls, including the highly recalcitrant lignin, are efficiently mineralized during white rot. Oxidative degradation of lignin is thought to involve extracellular peroxidases coupled to peroxide-generating oxidases. The white rot fungi also progressively deconstruct cellulose and hemicellulose using an array of glycoside hydrolases. In contrast, bulk lignin remains as a polymeric residue during brown rot, while cellulose is rapidly depolymerized. Substantial evidence has supported the involvement of low molecular weight, diffusible oxidants such as hydroxyl radical. Resilient brown rot residues contribute to the carbon pool in humic soils, particularly in boreal, conifer-dominated ecosystems. Uncertainty about the mechanisms of lignocellulose degradation has been an obstacle to understanding microbial interactions in forest soils and to the development of commercial processes dependent on bioconversions. Addressing the issue, collaborative efforts with the U.S. Department of Energy and universities have characterized the entire genome of several wood decay fungi. These genomes have reveal impressive sequence diversity, and recent functional analyses are providing a deeper understanding of plant cell wall deconstruction and the transformation of organopollutants. During FY2016, we identified hundreds of enzymes involved, directly or indirectly, in the conversion of recalcitrant lignocellulose to high value products. We examined fungal gene expression in response to specific poplar genotypes and small diameter lodgepole pine. These studies showed that substrate composition substantially altered gene expression suggesting that commercial enzyme mixtures could be tailored to specific woody substrates. Beyond this, newly available genome resources have substantially enhanced our knowledge of mechanisms of lignocellulose conversions and revealed new and novel enzymes with considerable potential in emerging technologies. Thus, the findings facilitate development of enzymatic systems for the efficient conversion of an expanding number of forest feedstocks. These results have been published in peer reviewed journals and presented by invitation to international audiences.
Impacts
Substantial effort focused on the conversion of woody material for industrial processes. This research addresses the identification/improvement of enzyme systems and the expansion of the number of suitable feedstocks. Our findings have identified specific enzymes key to the degradation of lignin, a recalcitrant polymer that interferes with efficient deconstruction and utilization of lignocellulosic biomass. In addition, the research has contributed to our understanding of cellulose depolymerization. These processes are central to forest carbon cycling, and novel fungi and enzymes have been discovered, some of which may aid bioprocess development.
Publications
- Daou, Marianne; Piumi, François; Cullen, Daniel; Record, Eric; Faulds, Craig B. 2016. Heterologous production and characterization of two glyoxal oxidases from Pycnoporus cinnabarinus. Applied and Environmental Microbiology. 82(16). 4867-4875.
- Gaskell, Jill; Blanchette, Robert A.; Stewart, Philip E.; BonDurant, Sandra Splinter; Adams, Marie; Sabat, Grzegorz; Kersten, Phil; Cullen, Dan. 2016. Transcriptome and secretome analyses of the wood decay fungus Wolfiporia cocos support alternative mechanisms of lignocellulose conversion. Applied and Environmental Microbiology. 82(13): 3979-3987.
- Hori, Chiaki; Cullen, Daniel. 2016. Prospects for bioprocess development based on recent genome advances in lignocellulose degrading basidiomycetes. In: Schmoll, Monika; Dattenbock, Christoph, eds. Gene Expression Systems in Fungi: Advancements and Applications. p. 161-181.
- Miettinen, Otto; Riley, Robert; Barry, Kerrie; Cullen, Dan; et al. 2016. Draft genome sequence of the white-rot fungus Obba rivulosa 3A-2. Genome Announcements. 4(5): 1-2.
- Skyba, Oleksandr; Cullen, Dan; Douglas, Carl J.; Mansfield, Shawn D. 2016. Gene expression patterns of wood decay fungi Postia placenta and Phanerochaete chrysosporium are influenced by wood substrate composition during degradation. Applied and Environmental Microbiology. 82(14): 4387-4400.
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Progress 10/01/14 to 09/30/15
Outputs
OUTPUTS: Wood and litter degradation is a critical component of the carbon cycle, that impacts soil productivity, and has the potential to be exploited for the production of biofuels and other green technologies. Two categories of wood decay chemistries, white rot and brown rot, have long been recognized. White rot fungi degrade all components of plant cell walls, including the highly recalcitrant lignin fraction. The degradation of lignin is an oxidative process thought to involve extracellular peroxidases coupled to peroxide-generating oxidases. White rot fungi also employ a diverse array of glycoside hydrolases to progressively deconstruct cellulose and hemicellulose. In contrast, Brown rot fungi modify but do not appreciably remove lignin, which remains as a polymeric residue. Brown rot fungi rapidly depolymerize cellulose and considerable evidence has implicated low molecular weight, diffusible oxidants such as hydroxyl radical. Brown rot residues resist further decay and contribute to the carbon pool in humic soils, particularly in cool-temperate and boreal, conifer-dominated ecosystems. Irrespective of their importance as key components of forest ecosystems and as potential sources of novel enzymes, mechanisms underlying lignocellulose deconstruction and substrate preference are obscure. This uncertainty has been an obstacle to understanding microbial interactions in forest soils and to the development of processes dependent on bioconversions. Addressing these issues, newly available genome resources have opened new areas of research. Our examination of transcript and proteome profiles has elucidated the importance of specific enzymes in the metabolism of troublesome extractives commonly associated with conifers. Published in the prestigious peer-reviewed journal, PLoS Genetics, the latter research involved collaborative efforts with the U.S. Department of Energy and an international consortium of research organization. Ultimately, the findings may expand the utility of forestry feedstocks. During FY2015, we identified hundreds of enzymes involved, directly or indirectly, in the conversion of recalcitrant lignin in wood. These results were presented at several international conferences and in the peer-reviewed journal Applied and Environmental Microbiology. In FY2015 we also began systematic analyses of forest soils using deep sequence techniques commonly referred to as metagenomics and metatranscriptomics. These studies are part of a large international consortium seeking to define microbial community structure and function in diverse forest ecosystems. Our activities focus on fire disturbed sites in Western forests. Critical analyses of bioinformatic approaches to these large datasets were discussed at a workshop sponsored by Los Alamos National Laboratories. A paper describing the computational options was published in the peer-reviewed journal Fungal Ecology.
Impacts
Considerable worldwide attention is currently focused on utilizing woody material for bioenergy processes. Much of this emphasis is on identification/improvement of enzyme systems, expanding the number of suitable feedstocks, and development of practical pretreatment processes. Our results provide insight into the metabolism of extractives and thereby illuminate a path toward more effective use of conifers. Other findings have identified specific enzymes key to the degradation of liginin, a recalcitrant polymer that interferes with efficient deconstruction and utilization of lignocellulosic biomass. Separate studies of soil microbiology in fire disturbed Western forests will advance understanding of the role of fungi that influence the emergence of uniform lodgepole pine stands. Detailed interactions among plant symbionts, pathogens and lignocellulose-degrading saprophytes are being revealed and, ultimately, the results may impact management decisions. In addition, novel fungi and enzymes are being discovered, some of which may aid bioenergy-related processes.
Publications
- Hori, Chiaki; Ishida, Takuya; Igarashi, Kiyohiko; Samejima, Masahiro; Suzuki, Hitoshi; Master, Emma; Ferreira, Patricia; Ruiz-Duenas, Francisco J.; Held, Benjamin; Canessa, Paulo; Larrondo, Luis F.; Schmoll, Monika; Druzhinina, Irina S.; Kubicek, Christian P.; Gaskell, Jill A.; Kersten, Phil; St. John, Franz; Glasner, Jeremy; Sabat, Grzegorz; Bondurant, Sandra Splinter; Syed, Khajamohiddin; Yadav, Jagjit; Mgbeahuruike, Anthony C.; Kovalchuk, Andriy; Asiegbu, Fred O.; Lackner, Gerald; Hoffmeister, Dirk; Recoret, Jorge; Gutierrez, Ana; Sun, Hui; Lindquist, Erika; Barry, Kerrie; Riley, Robert; Grigoriev, Igor V.; Henrissat, Bernard; Kues, Ursula; Berka, Randy M.; Martinez, Angel T.; Covert, Sarah F.; Blanchette, Robert A.; Cullen, Daniel 2014. Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood. PLOS Genet Volume 10, Number 12, December 2014; 20 p.
- Kuske, Cheryl R.; Hesse, Cedar N.; Challacombe, Jean F.; Cullen, Daniel; Herr, Joshua R.; Mueller, Rebecca C.; Tsang, Adrian; Vilgalys, Rytas 2015. Prospects and challenges for fungal metatranscriptomics of complex communities. Fungal Ecology, Corrected proof. 5p.
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Progress 10/01/13 to 09/30/14
Outputs
OUTPUTS: Common inhabitants of forest ecosystems, wood decay fungi play a key role recycling the enormous reservoirs of carbon in dead trees, litter and below ground. The degradative processes are essential for maintaining forest health through nutrient mobilization and through interactions with beneficial and pathogenic microbes. Efficient breakdown of the major components of wood (cellulose, hemicellulose and lignin) requires the concerted action of enzymes possessed by a relatively small group of filamentous fungi. These enzyme systems show considerable promise in biofuels production and in organopollutant remediation technologies. However, the precise mechanisms underlying such processes are poorly understood, and this poses a signficant obstacle to biotechnological exploitation. Addressing the issue, our collaborative efforts with the U.S. Department of Energy and an international consortium of research organizations have characterized the entire genome of several wood decay fungi. These genomes have revealed impressive sequence diversity, and recent functional analyses are providing a deeper understanding of plant cell wall deconstruction and the transformation of organopollutants. During FY2014, we identified hundreds of enzymes involved, directly or indirectly, in the conversion of recalcitrant lignocellulose to high value products. In one project, we examined fungal gene expression in response to specific plant host genotypes such as hybrid poplar and transgenic derivatives. These studies showed that lignin composition substantially altered gene expression suggesting that commercial enzyme mixtures could be improved by tailoring enzyme components to specific forestry feedstocks. The findings facilitate development of enzymatic systems for biomass conversions and help guide Populus breeding programs. A separate study revealed that the mechanism(s) of lignin oxidation likely involve hitherto unknown biochemical pathways, thereby opening new areas of investigation. Results were disseminated in high-impact publications, including the prestigious peer-reviewed journal Proceeding of the National Academy of Science. Research findings were also featured in invited presentations before the annual BioEnergy Basic Conference, Noordwijkerhout, Netherlands, the annual Mycological Society of America Conference, Michigan State University, and the 5th International Symposium on Advanced Energy Science, Kyoto, Japan.
Impacts
Our findings advance fundamental understanding of lignocellulose conversions and pave the way for whole new areas of research. Addressing key barriers in the utilization of forestry feedstocks, processes and specific enzymes required for efficient cell wall deconstruction were identified. Such bioconversions generate small molecular weight products that will expand the utility of low cost forestry resources for biofuels and high value biochemicals. Much worldwide effort is currently focused on improving wood utilization, particularly through identification/improvement of enzyme systems, genetic alterations in plant cell wall composition, and development of pretreatment processes. Our results demonstrate the importance of host genotype, at least with respect to lignin composition. The findings suggest that commercial enzyme mixtures could be improved by tailoring enzyme components to specific feedstocks. The information gained may facilitate further development of enzymatic systems for biomass treatment and help guide Populus breeding programs.
Publications
- Hori, Chiaki; Gaskell, Jill; Igarashi, Kiyohiko; Kersten, Phil; Mozuch, Michael; Samejima, Masahiro; Cullen, Dan 2014. Temporal Alterations in the Secretome of the Selective Ligninolytic Fungus Ceriporipsis subvermispora during growth on Aspen Wood Reveal this Organism's Strategy for Degrading Lighnocellulose. Appl. Environ. Microbiol. 2014, Volume 80, Number 7, pp. 2062-2070.
- Riley, Robert; Salamov, Asaf A.; Brown, Daren W.; Nagy, Laszlo G.; Floudas, Dimitrios; Held, Benjamin W.; Levasseur, Anthony; Lombard, Vincent; Morin, Emmanuelle; Otillar, Robert; Lindquist, Erika A.; Sun, Hui; LaButti, Kurt M.; Schmutz, Jeremy; Jabbour, Dina; Luo, Hong; Baker, Scott E.; Pisabarro, Antonio G.; Walton, Jonathan D.; Blanchette, Robert A.; Henrissat, Bernard; Martin, Francis; Cullen, Daniel; Hibbett, David S.; Grigoriev, Igor V.2014. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. PNAS, July 8, 2014, Volume 111, Number 27, 2014; pp.9923-9928.
- Gaskell, Jill; Marty, Amber; Mozuch, Michael; Kersten, Philip J.; Bondurant, Sandra Splinter; Sabat, Grzegorz; Azarpira, Ali; Ralph, John; Skyba, Oleksandr; Mansfield, Shawn D.; Blanchette, Robert A.; Cullen, Dan 2014. Influence of Populus Genotype on Gene Expression by the Wood Decay Fungus Phanerochaete chrysosporium. Appl. Environ. Microbiol. 2014, Volume 80, Number 18, 2014; pp. 5828-5835.
- Hadar, Yitzhak; Cullen, Daniel 2013. Chapter 5: Organopollutant Degradation by Wood Decay Basidiomycetes. Hadar, Y., and Cullen, D. (2013) Organopollutant degradation by wood decay basidiomycetes. In: The Mycota, Agricultural Applications (Kempken, F. ed.), 2 Ed., Springer-Verlag, Berlin. 2013; pp. 115-144.
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Progress 10/01/12 to 09/30/13
Outputs
OUTPUTS: Decay fungi are common inhabitants of forest ecosystems where they play a pivotal role recycling enormous reservoirs of carbon below ground, in dead trees and litter. The degradative processes are essential for nutrient mobilization and maintaining forest health. Some of these fungi also provide benefits through mycorrhiza interactions while others are highly destructive tree pathogens. Still others play a crucial role in the transformation and degradation of humic substances, a major fraction of soil organic matter. Irrespective of their ecological importance, the genetic and physiological mechanisms underlying these processes are poorly understood, and this poses a signficant barrier to biotechnological exploitation of these unique microbes. Addressing this issue during FY13, our collaborative efforts with the U.S. Department of Energy and an international assortment of academic laboratories have substantially contributed to our understanding of wood- and litter-decomposing fungi. Among thousands of newly discovered genes, we have identified dozens of enzymes potentially useful for the conversion of lignocellulosics to small molecular weight products and to recalcitrant humic substances. These enzymatic transformations offer considerable promise in emerging bioprocesses related to biofuels production and to organopollutant remediation technologies. Results were disseminated in international conference proceedings and in influential peer-reviewed journals. Our findings also pave the way for fundamental investigations of microbial communities in fire-disturbed Western forests. Performed in collaboration with the Department of Energy and an international consortium of researchers, these studies are elucidating the key microbes involved in the establishment of lodgepole pine stands following catastrophic fire. This in turn may lead to improved management practices.
Impacts
Our findings advance knowledge of basic mechanisms of lignocellulose degradation, a pivotal aspect of carbon cycling in forest ecosystems. Processes and specific enzymes involved in efficient cell wall deconstruction, a key obstacle in the utilization of forestry feedstocks, were clarified. Conversions to small molecular weight compounds will expand the utility of low cost forestry resources for biofuels and high value biochemicals. Our analysis of litter-decomposing fungi also revealed unexpected diversity of oxidative enzymes likely involved in soil composition and possibly valuable for degrading recalcitrant organopollutants. Beyond applications, the findings advance fundmental understanding of the ecology and evolution of the lignocellulose degrading fungi. Considered together with ongoing studies of microbial communities in Western forests, an integrated view of fire disturbed ecosystems is emerging.
Publications
- Doddapaneni, Harshavardhan; Subramanian, Venkataramanan; Fu, Bolei; Cullen, Dan. 2013. A comparative genomic analysis of the oxidative enzymes potentially involved in lignin degradation by Agaricus bisporus. Fungal Genetics and Biology. 55: 22-31.
- Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R.; Foulongne-Oriol, Marie; Lombard, Vincent; Nagy, Laszlo G.; Ohm, Robin A.; Patyshakuliyeva, Aleksandrina; Brun, Annick; Aerts, Andrea L.; Bailey, Andrew M.; Billette, Christophe; Coutinho, Pedro M.; Deakin, Greg; Doddapaneni, Harshavardhan; Floudas, Dimitrios; Grimwood, Jane; Hilden, Kristiina; Kues, Ursula; LaButti, Kurt M.; Lapidus, Alla; Lindquist, Erika A.; Lucas, Susan M.; Murat, Claude; Riley, Robert W.; Salamov, Asaf A.; Schmutz, Jeremy; Subrananian, Venkataramanan; Wosten, Han A.B.; Xu, Jianping; Eastwood, Daniel C.; Foster, Gary D.; Sonnenberg, Anton S.M.; Cullen, Daniel; de Vries, Ronald P.; Lundell, Taina; Hibbett, David S.; Henrissat, Bernard; Burton, Kerry S.; Kerrigan, Richard W.; Challen, Michael P.; Grigoriev, Igor V.; Martin, Francis. 2012. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proceedings of the National Academy of Science. 109(43): 17501⿿17506.
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