RNA extraction and sequencing
Sediment was thawed within minutes inside the cryotubes and ~2 g of material was added into the RNeasy PowerSoil bead tubes and was extracted using the same kit (RNeasy PowerSoil, QIAGEN). After RNA extraction, any remaining DNA was removed with DNase treatment using the TURBO DNA-free kit (Invitrogen), followed by bacterial rRNA depletion using the RiboMinus Transcriptome Isolation Kit (bacteria version, ThermoFisher Scientific). Library preparation followed the TruSeq RNA Library Prep v2 kit (Illumina) without including the poly-A selection step. The samples were sequenced at the Science for Life Laboratory, Stockholm on a single Illumina NovaSeq6000 S4 lane using paired-end 2 × 150 bp read technology. A full list of sample names, sequences yielded, quality scores, read lengths etc. are available in Supplementary Data 1.