Browsing by Subject "PLANT BIOMASS"

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  • Daly, Paul; Lopez, Sara Casado; Peng, Mao; Lancefield, Christopher S.; Purvine, Samuel O.; Kim, Young-Mo; Zink, Erika M.; Dohnalkova, Alice; Singan, Vasanth R.; Lipzen, Anna; Dilworth, David; Wang, Mei; Ng, Vivian; Robinson, Errol; Orr, Galya; Baker, Scott E.; Bruijnincx, Pieter C. A.; Hilden, Kristiina S.; Grigoriev, Igor V.; Mäkelä, Miia R.; de Vries, Ronald P. (2018)
    White-rot fungi, such as Dichomitus squalens, degrade all wood components and inhabit mixed-wood forests containing both soft- and hardwood species. In this study, we evaluated how D. squalens responded to the compositional differences in softwood [guaiacyl (G) lignin and higher mannan content] and hardwood [syringyl/guaiacyl (S/G) lignin and higher xylan content] using semi-natural solid cultures. Spruce (softwood) and birch (hardwood) sticks were degraded by D. squalens as measured by oxidation of the lignins using 2D-NMR. The fungal response as measured by transcriptomics, proteomics and enzyme activities showed a partial tailoring to wood composition. Mannanolytic transcripts and proteins were more abundant in spruce cultures, while a proportionally higher xylanolytic activity was detected in birch cultures. Both wood types induced manganese peroxidases to a much higher level than laccases, but higher transcript and protein levels of the manganese peroxidases were observed on the G-lignin rich spruce. Overall, the molecular responses demonstrated a stronger adaptation to the spruce rather than birch composition, possibly because D. squalens is mainly found degrading softwoods in nature, which supports the ability of the solid wood cultures to reflect the natural environment.
  • Lundell, Taina K.; Mäkelä, Miia R.; de Vries, Ronald P.; Hilden, Kristiina S. (Academic Press, 2014)
    Advances in Botanical Research
    Saprobic (saprotrophic and saprophytic) wood-decay fungi are in majority species belonging to the fungal phylum Basidiomycota, whereas saprobic plant litter-decomposing fungi are species of both the Basidiomycota and the second Dikarya phylum Ascomycota. Wood-colonizing white rot and brown rot fungi are principally polypore, gilled pleurotoid, or corticioid Basidiomycota species of the class Agaricomycetes, which also includes forest and grassland soil-inhabiting and litter-decomposing mushroom species. In this chapter, examples of lignocellulose degradation patterns are presented in the current view of genome sequencing and comparative genomics of fungal wood-decay enzymes. Specific attention is given to the model white rot fungus, lignin-degrading species Phanerochaete chrysosporium and its wood decay-related gene expression (transcriptomics) on lignocellulose substrates. Types of fungal decay patterns on wood and plant lignocellulose are discussed in the view of fungal lifestyle strategies. Potentiality of the plant biomass-decomposing Basidiomycota species, their secreted enzymes and respective lignocellulose-attacking genes is evaluated in regard to development of biotechnological and industrial applications.
  • Mäkelä, Miia R.; Aguilar-Pontes, Maria Victoria; van Rossen-Uffink, Diana; Peng, Mao; de Vries, Ronald P. (2018)
    In nature, the fungus Aspergillus niger degrades plant biomass polysaccharides to monomeric sugars, transports them into its cells, and uses catabolic pathways to convert them into biochemical building blocks and energy. We show that when grown in liquid cultures, A. niger takes up plant-biomass derived sugars in a largely sequential manner. Interestingly, this sequential uptake was not mediated by the fungal general carbon catabolite repressor protein CreA. Furthermore, transcriptome analysis strongly indicated that the preferential use of the monomeric sugars is arranged at the level of transport, but it is not reflected in transcriptional regulation of sugar catabolism. Therefore, the results indicate that the regulation of sugar transport and catabolism are separate processes in A. niger.
  • Pontes, Maria Victoria Aguilar; Patyshakuliyeva, Aleksandrina; Post, Harm; Jurak, Edita; Hilden, Kristiina; Altelaar, Maarten; Heck, Albert; Kabel, Mirjam A.; de Vries, Ronald P.; Mäkelä, Miia R. (2018)
    The white button mushroom Agaricus bisporus is one of the most widely produced edible fungus with a great economical value. Its commercial cultivation process is often performed on wheat straw and animal manure based compost that mainly contains lignocellulosic material as a source of carbon and nutrients for the mushroom production. As a large portion of compost carbohydrates are left unused in the current mushroom cultivation process, the aim of this work was to study wild-type A. bisporus strains for their potential to convert the components that are poorly utilized by the commercial strain A15. We therefore focused our analysis on the stages where the fungus is producing fruiting bodies. Growth profiling was used to identify A. bisporus strains with different abilities to use plant biomass derived polysaccharides, as well as to transport and metabolize the corresponding monomeric sugars. Six wild-type isolates with diverse growth profiles were compared for mushroom production to A15 strain in semi-commercial cultivation conditions. Transcriptome and proteome analyses of the three most interesting wild-type strains and A15 indicated that the unrelated A. bisporus strains degrade and convert plant biomass polymers in a highly similar manner. This was also supported by the chemical content of the compost during the mushroom production process. Our study therefore reveals a highly conserved physiology for unrelated strains of this species during growth in compost.