Differences in Soil Fungal Communities between European Beech (Fagus sylvatica L.) Dominated Forests Are Related to Soil and Understory Vegetation

Abstract

Fungi are important members of soil microbial communities with a crucial role in biogeochemical processes. Although soil fungi are known to be highly diverse, little is known about factors influencing variations in their diversity and community structure among forests dominated by the same tree species but spread over different regions and under different managements. We analyzed the soil fungal diversity and community composition of managed and unmanaged European beech dominated forests located in three German regions, the Schwäbische Alb in Southwestern, the Hainich-Dün in Central and the Schorfheide Chorin in the Northeastern Germany, using internal transcribed spacer (ITS) rDNA pyrotag sequencing. Multiple sequence quality filtering followed by sequence data normalization revealed 1655 fungal operational taxonomic units. Further analysis based on 722 abundant fungal OTUs revealed the phylum Basidiomycota to be dominant (54%) and its community to comprise 71.4% of ectomycorrhizal taxa. Fungal community structure differed significantly (p≤0.001) among the three regions and was characterized by non-random fungal OTUs co-occurrence. Soil parameters, herbaceous understory vegetation, and litter cover affected fungal community structure. However, within each study region we found no difference in fungal community structure between management types. Our results also showed region specific significant correlation patterns between the dominant ectomycorrhizal fungal genera. This suggests that soil fungal communities are region-specific but nevertheless composed of functionally diverse and complementary taxa.

Stand structure and deadwood amount influences saproxylic fungal biodiversity in Mediterranean mountain unmanaged forests

“…In the studied stands, the high fungal diversity and abundance was expected because of the reduced anthropic disturbance. Nevertheless, an analogous trend in fungal diversity was also observed by Wubet et al (2012), which compared many European beech forest soils characterized by different management types. They found no differences in the fungal community structure, suggesting that soil fungal communities are region-specific, though composed of functionally diverse and complementary taxa.…”

Linking molecular deadwood-inhabiting fungal diversity and community dynamics to ecosystem functions and processes in Central European forests

“…All DNA extracts from the wood samples of each log were pooled into a composite extract prior to PCR. Fungal ITS rDNA amplicon libraries were produced as described in Wubet et al (2012). Briefly we used fusion primers designed with pyrosequencing primer B, a barcode and the fungal specific primer ITS1-F (Gardes and Bruns 1993) as a forward primer and pyrosequencing primer A and the universal eukaryotic primer ITS4 (White et al 1990) as a reverse primer to amplify the fungal nuclear ribosomal internal transcribed spacer (nrITS) rDNA.…”

“…To avoid sampling size effects, the number of reads per sample was normalized for each data set by randomly subsampling to the lower number of reads per samples using the subsample script as implemented in MOTHUR. The sequence dataset was then clustered and assigned to OTUs using CD-HIT-EST of the CD-HIT package version 4.5.4 (Li and Godzik 2006) at a 97 % threshold of pairwise sequence similarity as in Wubet et al (2012). We used MOTHUR to taxonomically assign representative sequences of the OTUs against the UNITE reference database (as downloaded in May 2013) using the default set-up (Abarenkov et al 2010).…”

Functional land-use change effects on soil fungal communities in Chilean temperate rainforests

“…To reduce sequencing errors, multiple levels of sequence processing and quality filtering were performed as described in Wubet et al (2012). Flowgrams were extracted according to 100% barcode similarity; reads with an average quality score of < 25, read length of < 200 bp, and ambiguous bases and homopolymers of > 8 bases were removed and barcodes and primers were trimmed using the split libraries script available in the "Quantitative Insights…”