Linking fungal communities to wood density loss after 12 years of log decay.

Changes in biodiversity might alter decomposition processes and, consequently, carbon and nutrient cycling. We examined fungal diversity and density loss in experimental Norway spruce logs after 12 years of decay in a hemiboreal forest. Between 28 and 50% of the original wood biomass remained, depending on the fungal community composition in the log, operational taxonomic unit (OTU) richness had only a minor effect on the log biomass. Although the communities were OTU rich (190-340 OTUs per log), the majority of OTUs were infrequent or rare; wood degradation therefore depended mostly on the most abundant OTUs and their decomposing abilities. The least decayed logs were characterized by continuous dominance of an earlier colonizer and by high within-log community diversity, which was significantly related to sample variables (position in log, density and moisture). In the most decayed logs, the earlier colonizers were generally replaced by white-rot species able to exploit the highly decomposed wood. The communities were relatively spatially uniform within whole logs, independent of the sample variables, whereas among-log diversity was high. Importance of fungal community composition in decomposition processes should be taken into account when studying and modeling carbon dynamics in forest ecosystems.

Diverse ecological roles within fungal communities in decomposing logs of Picea abies.

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.

New primers to amplify the fungal ITS2 region--evaluation by 454-sequencing of artificial and natural communities.

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.

Diversity and decomposing ability of saprophytic fungi from temperate forest litter.

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.

Microbial diversity during cellulose decomposition in different forest stands: I. microbial communities and environmental conditions.

We studied the effect of forest tree species on a community of decomposers that colonize cellulose strips. Both fungal and bacterial communities were targeted in a native forest dominated by beech and oak and 30-year-old beech and spruce plantations, growing in similar ecological conditions in the Breuil-Chenue experimental forest site in Morvan (France). Microbial ingrowths from the 3rd to 10th month of strip decomposition (May to December 2004) were studied. Community composition was assessed using temperature gradient gel electrophoresis with universal fungal (ITS1F, ITS2) and bacterial (1401r, 968f) primers. Soil temperature and moisture as well as fungal biomass were also measured to give additional information on decomposition processes. Changing the dominant tree species had no significant influence in the number of decomposer species. However, decomposer community composition was clearly different. If compared to the native forest, where community composition highly differed, young monocultures displayed similar species structure for fungi and bacteria. Both species numbers and community composition evolved during the decay process. Time effect was found to be more important than tree species. Nevertheless, the actual environmental conditions and seasonal effect seemed to be even more determining factors for the development of microbial communities. The course and correlations of the explored variables often differed between tree species, although certain general trends were identified. Fungal biomass was high in summer, despite that species richness (SR) decreased and conversely, that high SR did not necessarily mean high biomass values. It can be concluded that the growth and development of the microbiological communities that colonized a model material in situ depended on the combination of physical and biological factors acting collectively and interdependently at the forest soil microsite.