Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil

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Abstract

We used paddy soil slurries amended with rice straw to identify the microbial populations involved in the methanogenic breakdown of plant polymers. Rice straw greatly stimulated microbial activity over the 28-day incubation period. On day 7, the transient peak concentration of acetate (24 mM) coincided with the onset of increased methane production. Microbial 16S rRNA transcript numbers increased by one to two orders of magnitude, but not the 16S rRNA gene copy numbers. Using metatranscriptomic rRNA,Clostridiaceae,Lachnospiraceae,Ruminococcaceae,VeillonellaceaeandPseudomonadaceaewere identified to be the most abundant and the most dynamic bacterial groups. Changes in methanogen rRNA and mRNA abundances corresponded well with methanogenic activity. Acetate determined the abundance ratio betweenMethanosarcinaceaeandMethanosaetaceae.Methanocellaceaedominated hydrogenotrophic methanogenesis. Transcript levels of mRNA families involved in plant polymer breakdown increased slightly with time. Glycosyl hydrolase (GH) transcripts involved in cellulose and chitin breakdown were predominantly expressed by theFirmicutes, whereas those involved in hemicellulose breakdown exhibited more diverse taxonomic sources, includingAcidobacteria,BacteriodetesandChloroflexi. Taken together, we observed strong population dynamics and the expression of taxonomically diverse GH families, suggesting that not onlyFirmicutes, but also less abundant groups play a major functional role in the decomposition of rice straw.

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