Data for: The impact of spatial isolation and local habitat conditions on colonization of recent forest stands by ectomycorrhizal fungi

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Boeraeve, Margaux
Community Ecology; Mycology; Forest Ecology
data summary

In this study, we selected 17 recently established (between 18 and 45 years old) forest stands and nine ancient forest stands (continuous forest land use since at least 1775) across Flanders (Northern Belgium). Nine of the recent forest stands were adjacent to ancient forest, and 8 were isolated from ancient forests (minimum, median and maximum distance from ancient forest: respectively 219, 1901 and 7605 m). The recent forest stands were all homogeneous stands of Quercus robur planted on former agricultural land, while the tree layer of the ancient forest stands was dominated by Q. robur, with admixtures of other tree species (Acer pseudoplatanus, Betula pendula, Castanea sativa, Fagus sylvatica, Tilia sp. and Q. rubra). In each stand, a 10x10m plot was established in such a way that only Q. robur was present in and around the plot. In each plot, 10 soil cores were randomly taken with a narrow-bladed gouge auger (diameter 3 cm). The F, H and A horizon, depth 0-15 cm were collected. The samples were pooled in two composite soil samples (five soil cores pooled in one sample, resulting in two samples per plot). Roots from oak (Quercus robur) were isolated from all samples, brushed to remove remaining soil particles and 0.25 g of root per sample was used to extract DNA using the Power Soil DNA Isolation Kit. After DNA extraction, the ITS1 region of the nuclear ribosomal RNA genes was amplified using modified versions of the primer set ITS1F and ITS2. After PCR, gel electrophoresis and purification from gel, samples were pooled and sent for 250bp paired-end sequencing on an Illumina Miseq. Raw sequence data was submitted to NCBI SRA (Bioproject PRJNA477418). The demultiplexed reads provided by Genomics Core UZ Leuven were quality filtered, clustered into OTUs and assigned a taxonomy through the PIPITS pipeline. Representative sequences that could not be assigned a taxonomy at genus-level were subjected to a BLAST-search against the NCBI nucleotide database. Sequences from environmental or uncultured samples were excluded from the results and the ten best matches with maximum e-value e-100 and minimum sequence similarity of 90% (genus level) and 97% (species level) were used to assign a taxonomy. In an additional quality filtering step, OTUs represented by less than 0.01% of the reads in a sample were considered absent from that sample. Finally, the results were put in an OTU table, which was run through FUNGuild, in order to select the ectomycorrhizal OTUs from the dataset. Rarefaction curves were fitted in order to check whether they were sufficiently deep sequenced. Samples of which the rarefaction curve did not reach an asymptote were removed. If the two samples from the same plot still remained after the removal, their results were merged by averaging their read numbers. Nitrate, ammonium, plant available phosphorus, pH, gravimetric water content and organic carbon content were analyzed for each of the two composite soil samples.