With recent methodological advances, molecular markers are increasingly used for semi‐quantitative analyses of fungal communities. The aim to preserve quantitative relationships between genotypes through PCR places new demands on primers to accurately match target sites and provide short amplicons. The internal transcribed spacer (ITS) region of the ribosome encoding genes is a commonly used marker for many fungal groups. Here, we describe three new primers – fITS7, gITS7 and fITS9, which may be used to amplify the fungal ITS2 region by targeting sites in the 5.8S encoding gene. We evaluated the primers and compared their performance with the commonly used ITS1f primer by 454‐sequencing of both artificially assembled templates and field samples. When the entire ITS region was amplified using the ITS1f/ITS4 primer combination, we found strong bias against species with longer amplicons. This problem could be overcome by using the new primers, which produce shorter amplicons and better preserve the quantitative composition of the template. In addition, the new primers yielded more diverse amplicon communities than the ITS1f primer.

Owing to previous methodological limitations, knowledge about the fine-scale distribution of fungal mycelia in decaying logs is limited. We investigated fungal communities in decaying Norway spruce logs at various spatial scales at two environmentally different locations in Sweden. On the basis of 454 pyrosequencing of the ITS2 region of rDNA, 1914 operational taxonomic units (OTUs) were detected in 353 samples. The communities differed significantly among logs, but the physical distance between logs was not found to have a significant effect on whether fungal communities had any resemblance to each other. Within a log, samples that were closer together generally had communities that showed more resemblance to each other than those that were further apart. OTUs characteristic for particular positions on the logs could be identified. In general, these OTUs did not overlap with the most abundant OTUs, and their ecological role was often unknown. Only a few OTUs were detected in the majority of logs, whereas numerous OTUs were rare and present in only one or a few logs. Wood-decaying Basidiomycetes were often represented by higher sequence reads in individual logs than Ascomycete OTUs, suggesting that Basidiomycete mycelia spread out more rapidly when established. OTU richness tended to increase with the decay stage of the sample; however, the known wood decayers were most abundant in less-decomposed samples. The fungi identified in the logs represented different ecological strategies. Our findings differ from previously published sporocarp studies, indicating that the highly abundant fruiting species may respond to environment in different ways than the rest of the fungal community.

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This study was designed to examine saprophytic fungi diversity under different tree species situated in the same ecological context. Further, the link between the diversity and decomposition rate of two broadleaved, two coniferous and two mixed broadleaved-coniferous litter types was targeted. Litter material was decomposed in litter bags for 4 and 24 months to target both early and late stages of the decomposition. Fungal diversity of L and F layers were also investigated as a parallel to the litter bag method. Temperature gradient gel electrophoresis fingerprinting was used to assess fungal diversity in the samples. Mass loss values and organic and nutrient composition of the litter were also measured. The results showed that the species richness was not strongly affected by the change of the tree species. Nevertheless, the community compositions differed within tree species and decomposition stages. The most important shift was found in the mixed litters from the litter bag treatment for both variables. Both mixed litters displayed the highest species richness (13.3 species both) and the most different community composition as compared to pure litters (6.3-10.7 species) after 24 months. The mass loss after 24 months was similar or greater in the mixed litter (70.5% beech-spruce, 76.2% oak-Douglas-fir litter) than in both original pure litter types. This was probably due to higher niche variability and to the synergistic effect of nutrient transfer between litter types. Concerning pure litter, mass loss values were the highest in oak and beech litter (72.8% and 69.8%) compared to spruce and D. fir (59.4% and 66.5%, respectively). That was probably caused by a more favourable microclimate and litter composition in broadleaved than in coniferous plantations. These variables also seemed to be more important to pure litter decomposition rates than were fungal species richness or community structure.

Fungal communities in Norway spruce (Picea abies) logs in two forests in Sweden were investigated by 454-sequence analyses and by examining the ecological roles of the detected taxa. We also investigated the relationship between fruit bodies and mycelia in wood and whether community assembly was affected by how the dead wood was formed. Fungal communities were highly variable in terms of phylogenetic composition and ecological roles: 1910 fungal operational taxonomic units (OTUs) were detected; 21% were identified to species level. In total, 58% of the OTUs were ascomycetes and 31% basidiomycetes. Of the 231 337 reads, 38% were ascomycetes and 60% basidiomycetes. Ecological roles were assigned to 35% of the OTUs, accounting for 62% of the reads. Wood-decaying fungi were the most common group; however, other saprotrophic, mycorrhizal, lichenized, parasitic and endophytic fungi were also common. Fungal communities in logs formed by stem breakage were different to those in logs originating from butt breakage or uprooting. DNA of specific species was detected in logs many years after the last recorded fungal fruiting. Combining taxonomic identification with knowledge of ecological roles may provide valuable insights into properties of fungal communities; however, precise ecological information about many fungal species is still lacking.