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Tree stumps are expected to be increasingly used for energy production in Fennoscandia, thus environmental consequences of stump removal from forest land must be assessed. Aim of this work was to compile available data on the efficacy of stump removal in eradication of root rot fungi (Heterobasidion, Armillaria, and Phellinus), and to review its potential impacts on establishment and productivity of next forest generation. Site disturbance and some technical and economical aspects are discussed, and needs for future research outlined in northern European context. The review demonstrates that stump removal from clear-felled forest areas in most cases results in, a) reduction of root rot in the next forest generation, b) improved seedling establishment, and c) increased tree growth and stand productivity. Observed disturbances caused to a site by stumping operations are normally acceptable. The available data strongly suggests that possibly many (if achievable, all) rot-containing stumps must be removed during harvesting of stumps. Provided equal availability, the priority should be given for stump removal from root rot-infested forest areas, instead of healthy ones. As most studies were done in North America and Britain, several questions must be yet answered under Fennoscandian conditions: a) if and to which extent the conventional stump removal for biofuel on clear-felled sites could reduce the occurrence of Heterobasidion and Armillaria in the next forest generation, b) what impact is it likely to have on survival of replanted tree seedlings, and c) what consequences will there be for growth and productivity of next forest generation.

A total of 57 naturally established Stereum sanguinolentum isolates was obtained from artificially wounded Picea abies stems in a forest area of 2 ha in Lithuania. Somatic incompatibility tests revealed 27 vegetative compatibility groups (VCGs) that contained 1â10 isolates. There was no spatial clustering of S. sanguinolentum VCGs within the forest area. The extent of S. sanguinolentum decay was analysed in 48 P. abies stems, 9â26 cm in diameter at breast height. Within 7 years of wounding, the length of S. sanguinolentum decay column in stems was 107â415 cm (291.5 ± 77.3 cm on average), lateral spread of the fungus at the butt was 38â307 cm2 (142.3 ± 66.8 cm2) and decayed proportion of the stem cross-section at the wound site (the butt) was 3â84% (36.8 ± 19.7%). In average, S. sanguinolentum VCG that infected 10 trees exhibited more slow growth inside the stem than VCGs that infected only one tree, and vertical growth varied to a greater extent within this VCG than among different VCGs. Correlation between stem diameter and vertical spread of S. sanguinolentum was not significant (r = â0.103). Despite uniformity of debarked area on all stems 7 years ago (300 cm2), open wound sizes on individual trees at the time of study were between 97â355 cm2 (215.1 ± 59.2 cm2) indicating large differences in wound healing capacity.

BACKGROUND: Adaptive processes shape the evolution of genomes and the diverse functions of different genomic regions are likely to have an impact on the trajectory and outcome of this evolution. The main underlying hypothesis of this study is that the evolution of Simple Sequence Repeats (SSRs) is correlated with the evolution of the genomic region in which they are located, resulting in differences of motif size, number of repeats, and levels of polymorphisms. These differences should be clearly detectable when analyzing the frequency and type of SSRs within the genome of a species, when studying populations within a species, and when comparing closely related sister taxa. By coupling a genome-wide SSR survey in the genome of the plant pathogenic fungus Heterobasidion irregulare with an analysis of intra- and interspecific variability of 39 SSR markers in five populations of the two sibling species H. irregulare and H. annosum, we investigated mechanisms of evolution of SSRs. RESULTS: Results showed a clear dominance of trirepeats and a selection against other repeat number, i.e. di- and tetranucleotides, both in regions inside Open Reading Frames (ORFs) and upstream 5 untranslated region (5UTR). Locus per locus AMOVA showed SSRs both inside ORFs and upstream 5UTR were more conserved within species compared to SSRs in other genomic regions, suggesting their evolution is constrained by the functions of the regions they are in. Principal coordinates analysis (PCoA) indicated that even if SSRs inside ORFs were less polymorphic than those in intergenic regions, they were more powerful in differentiating species. These findings indicate SSRs evolution undergoes a directional selection pressure comparable to that of the ORFs they interrupt and to that of regions involved in regulatory functions. CONCLUSIONS: Our work linked the variation and the type of SSRs with regions upstream 5UTR, putatively harbouring regulatory elements, and shows that the evolution of SSRs might be affected by their location in the genome. Additionally, this study provides a first glimpse on a possible molecular basis for fast adaptation to the environment mediated by SSRs.

Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non?lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.

Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli, the enzymes were shown to oxidize high redox potential substrates, but not Mn2. Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium.

Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato.We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified.A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production.Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.

Brown rot decay removes cellulose and hemicellulose from wood?residual lignin contributing up to 30percent of forest soil carbon?and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the ?dry rot? fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota