Browsing by Subject "Wood decay fungi"

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  • Mali, Tuulia; Mäki, Mari; Hellén, Heidi; Heinonsalo, Jussi; Bäck, Jaana; Lundell, Taina (2019)
    Effect of three wood-decaying fungi on decomposition of spruce wood was studied in solid-state cultivation conditions for a period of three months. Two white rot species (Trichaptum abietinum and Phlebia radiata) were challenged by a brown rot species (Fomitopsis pinicola) in varying combinations. Wood decomposition patterns as determined by mass loss, carbon to nitrogen ratio, accumulation of dissolved sugars, and release of volatile organic compounds (VOCs) were observed to depend on both fungal combinations and growth time. Similar dependence of fungal species combination, either white or brown rot dominated, was observed for secreted enzyme activities on spruce wood. Fenton chemistry suggesting reduction of Fe3+ to Fe2+ was detected in the presence of F. pinicola, even in co-cultures, together with substantial degradation of wood carbohydrates and accumulation of oxalic acid. Significant correlation was perceived with two enzyme activity patterns (oxidoreductases produced by white rot fungi; hydrolytic enzymes produced by the brown rot fungus) and wood degradation efficiency. Moreover, emission of four signature VOCs clearly grouped the fungal combinations. Our results indicate that fungal decay type, either brown or white rot, determines the loss of wood mass and decomposition of polysaccharides as well as the pattern of VOCs released upon fungal growth on spruce wood.
  • Mäkinen, Mari; Kuuskeri, Jaana; Laine, Pia; Smolander, Olli-Pekka; Kovalchuk, Andriy; Zeng, Zhen; Asiegbu, Fred; Paulin, Lars; Auvinen, Petri; Lundell, Taina (2019)
    Background The white rot fungus Phlebia radiata, a type species of the genus Phlebia, is an efficient decomposer of plant cell wall polysaccharides, modifier of softwood and hardwood lignin, and is able to produce ethanol from various waste lignocellulose substrates. Thus, P. radiata is a promising organism for biotechnological applications aiming at sustainable utilization of plant biomass. Here we report the genome sequence of P. radiata isolate 79 originally isolated from decayed alder wood in South Finland. To better understand the evolution of wood decay mechanisms in this fungus and the Polyporales phlebioid clade, gene content and clustering of genes encoding specific carbohydrate-active enzymes (CAZymes) in seven closely related fungal species was investigated. In addition, other genes encoding proteins reflecting the fungal lifestyle including peptidases, transporters, small secreted proteins and genes involved in secondary metabolism were identified in the genome assembly of P. radiata. Results The PACBio sequenced nuclear genome of P. radiata was assembled to 93 contigs with 72X sequencing coverage and annotated, revealing a dense genome of 40.4 Mbp with approximately 14 082 predicted protein-coding genes. According to functional annotation, the genome harbors 209 glycoside hydrolase, 27 carbohydrate esterase, 8 polysaccharide lyase, and over 70 auxiliary redox enzyme-encoding genes. Comparisons with the genomes of other phlebioid fungi revealed shared and specific properties among the species with seemingly similar saprobic wood-decay lifestyles. Clustering of especially GH10 and AA9 enzyme-encoding genes according to genomic localization was discovered to be conserved among the phlebioid species. In P. radiata genome, a rich repertoire of genes involved in the production of secondary metabolites was recognized. In addition, 49 genes encoding predicted ABC proteins were identified in P. radiata genome together with 336 genes encoding peptidases, and 430 genes encoding small secreted proteins. Conclusions The genome assembly of P. radiata contains wide array of carbohydrate polymer attacking CAZyme and oxidoreductase genes in a composition identifiable for phlebioid white rot lifestyle in wood decomposition, and may thus serve as reference for further studies. Comparative genomics also contributed to enlightening fungal decay mechanisms in conversion and cycling of recalcitrant organic carbon in the forest ecosystems.
  • 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.
  • Mali, Tuulia; Kuuskeri, Jaana; Shah, Firoz; Lundell, Taina Kristina (2017)
    Fomitopsis pinicola is a species of Polyporales frequently encountered in Nordic temperate and boreal forests. In nature, the fungus causes destructive brown rot in wood, colonizing tree trunks often occupied by other Basidiomycota species. We mimicked these species-species interactions by introducing F. pinicola to five white rot species, all common saprotrophs of Norway spruce. Hyphal interactions and mycelial growth in various combinations were recorded, while activities of lignocellulose-acting CAZymes and oxidoreductases were followed in co-cultures on two different carbon-source media. Of the species, Phlebia radiata and Trichaptum abietinum were the strongest producers of lignin-modifying oxidoreductases (laccase, manganese peroxidase) when evaluated alone, as well as in co-cultures, on the two different growth media (low-nitrogen liquid medium containing ground coniferous wood, and malt extract broth). F. pinicola was an outstanding producer of oxalic acid (up to 61 mM), whereas presence of P. radiata prevented acidification of the growth environment in the liquid malt-extract cultures. When enzyme profiles of the species combinations were clustered, time-dependent changes were observed on wood-supplemented medium during the eight weeks of growth. End-point acidity and production of mycelium, oxalic acid and oxidoreductase activities, in turn clustered the fungal combinations into three distinct functional groups, determined by the presence of F. pinicola and P. radiata, by principal component analysis. Our findings indicate that combinations of wood-decay fungi have dramatic dynamic effects on the production of lignocellulose-active enzymes, which may lead to divergent degradative processes of dead wood and forest litter.
  • Kuuskeri, Jaana Tuulia; Mäkelä, Miia Riitta; Isotalo, Jarkko Mikael; Oksanen, Ilona Maria; Lundell, Taina Kristina (2015)
    Background. The fungal genus Phlebia consists of a number of species that are significant in wood decay. Biotechnological potential of a few species for enzyme production and degradation of lignin and pollutants has been previously studied, when most of the species of this genus are unknown. Therefore, we carried out a wider study on biochemistry and systematics of Phlebia species. Methods. Isolates belonging to the genus Phlebia were subjected to four-gene sequence analysis in order to clarify their phylogenetic placement at species level and evolutionary relationships of the genus among phlebioid Polyporales. rRNA-encoding (5.8S, partial LSU) and two protein-encoding gene (gapdh, rpb2) sequences were adopted for the evolutionary analysis, and ITS sequences (ITS1 + 5.8S + ITS2) were aligned for in-depth species-level phylogeny. The 49 fungal isolates were cultivated on semi-solid milled spruce wood medium for 21 days in order to follow their production of extracellular lignocellulose-converting oxidoreductases and carbohydrate active enzymes. Results. Four-gene phylogenetic analysis confirmed the polyphyletic nature of the genus Phlebia. Ten species-level subgroups were formed, and their lignocellulose-converting enzyme activity profiles coincided with the phylogenetic grouping. The highest enzyme activities for lignin modification (manganese peroxidase activity) were obtained for Phlebia radiata group, which supports our previous studies on the enzymology and gene expression of this species on lignocellulosic substrates. Conclusions. Our study implies that there is a species-level connection of molecular systematics (genotype) to the efficiency in production of both lignocellulose-converting carbohydrate active enzymes and oxidoreductases (enzyme phenotype) on spruce wood. Thus, we may propose a similar phylogrouping approach for prediction of lignocellulose-converting enzyme phenotypes in new fungal species or genetically and biochemically less-studied isolates of the wood-decay Polyporales.
  • Mäkinen, Mari Annukka; Risulainen, Netta; Mattila, Hans Kristian; Lundell, Taina Kristina (2018)
    Previously identified twelve plant cell wall degradation-associated genes of the white rot fungus Phlebia radiata were studied by RT-qPCR in semi-aerobic solid-state cultures on lignocellulose waste material, and on glucose-containing reference medium. Wood-decay-involved enzyme activities and ethanol production were followed to elucidate both the degradative and fermentative processes. On the waste lignocellulose substrate, P. radiata carbohydrate-active enzyme (CAZy) genes encoding cellulolytic and hemicellulolytic activities were significantly upregulated whereas genes involved in lignin modification displayed a more complex response. Two lignin peroxidase genes were differentially expressed on waste lignocellulose compared to glucose medium, whereas three manganese peroxidase-encoding genes were less affected. On the contrary, highly significant difference was noticed for three cellulolytic genes (cbhI_1, eg1, bgl1) with higher expression levels on the lignocellulose substrate than on glucose. This indicates expression of the wood-attacking degradative enzyme system by the fungus also on the recycled, waste core board material. During the second week of cultivation, ethanol production increased on the core board to 0.24 g/L, and extracellular activities against cellulose, xylan, and lignin were detected. Sugar release from the solid lignocellulose resulted with concomitant accumulation of ethanol as fermentation product. Our findings confirm that the fungus activates its white rot decay system also on industrially processed lignocellulose adopted as growth substrate, and under semi-aerobic cultivation conditions. Thus, P. radiata is a good candidate for lignocellulose-based renewable biotechnology to make biofuels and biocompounds from materials with less value for recycling or manufacturing.