metatranscriptome analysis plant polymer breakdown paddy soil
For ribo-tag analyses, total RNA was extracted from collected soil and rice straw samples according to the method introduced by Mettel et al. (2010). RNA extracts were purified using the RNA clean and concentrator kit (Zymo Research). mRNA in purified extracts was selectiveley enriched by subtractive hybridisation using the RiboZero® rRNA removal kit (Meta-Bacteria) (Epicentre). Enriched mRNA was purified and quantified by fluorometry. The efficiency of rRNA removal was assessed by high-resolution gel electrophoresis using RNA HighSens Chips in a Bio-Rad Experion® (Bio-Rad). Enriched mRNA was reverse transcribed into cDNA and barcoded applying the NEBNext mRNA Sample Prep Master Mix Set 2 for 454 kit (New England Biolabs) following the manufacturers instructions. The fragment size range of individual libraries was assessed using the FlashGel system (Lonza) equipped with 1.2% DNA FlashGel cassettes. Libraries were quantified by fluorometry.     Used adaptor for barcoding:  ==========================  RL9 : paddy soil 1 day  RL10 : rice straw 1 day  RL11 : paddy soil 7 days  RL12 : rice straw 7 days