Fungi sequence data

Primers used for PCR amplification of bacteria and archaea 16S rRNA genes, ciliate protozoa 18S rRNA genes and anaerobic fungi ITS1 genes were designed in silico using ecoPrimers, the OBITools software suite (http://www.grenoble.prabi.fr/trac/OBITools) and a database created from sequences stored in GenBank. PCR amplicons were combined in equal volumes and purified (QIAquick PCR purification kit, Qiagen, Germany). After library preparation using a standard protocol with only five PCR cycles, amplicons were sequenced using the MiSeq technology from Illumina (Fasteris, SA, Geneva, Switzerland), which produced 250-base paired-end reads for all markers, other than for archaea (100-base paired-end reads). Alignment of paired-end reads, sample assignment and removal of sequences with ambiguous nucleotides and sequences of lengths outside the empirical sequence length distribution were performed with the OBITools software suite. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx', that is also part of this Dryad data package.