RNA extraction (NucleoBond RNA Soil Mini Kit; Macherey-Nagel, Germany), DNase digestion (RapidOut DNA Removal kit; Thermo Fisher Scientific, USA), cDNA transcription (Zymos Clean & Concentrator-5; Zymo, USA), primer addating at V3 and V4 hypervariable region of bacterial 16S rRNA and V4 and V5 for archaea 16S rRNA, PCA amplification (Kapa Hifi HotStart Ready Mix; Kapa Biosystems, USA), Ilumina sequencing adapters (Nextera XT Index Kit; Ilumina, USA), equimolar pooling for paired-end sequencing in a 2x300 bp run on the Ilumina MiSeq platform (Ilumina, USA)