Samples for the assessment of the metatranscriptome were fixed in situ and ribosomal RNA was depleted before sequencing. DNA and RNA were extracted using AllPrep DNA/RNA Kit from QIAGEN (Hilden, Germany). Samples for RNA sequencing were reverse transcribed with Multiscribe RT (Thermo Fisher Scientific, Waltham, MA, USA) after DNase treatment with TURBA-DNA-free Kit (Thermo Fisher Scientific, Waltham, MA, USA). Sequencing was done with Fasteris (Metatranscriptome, Illumina HiSeq 2500, Plain-Les-Ouates, Switzerland).