Metatranscriptome response of paddy soil microbial communities to salt stress

Salt stress strongly inhibited CH4, CO2 production and acetate consumption in a paddy soil model system after salt stress treatment. In addition, we investigated structure and function of the microbial communities in response to salt stress using metatranscriptomics. Bacterial, archaeal 16S rRNA genes and 16S rRNA, and mcrA were determined using quantative PCR and RT-PCR. In contray to a decrease of gene copy numbers, we observed a relative abundance increase of Clostridiaceae, Methanosarcinaceae and Methanobacteriaceae, and a decrease of Ruminococcaceae, Peptococcaceae, Veillonellaceae, Syntrophomonadaceae and Methanocellaceae under salt stress using metatranscriptomics. Lachnospiraceae were enriched at 300 mM NaCl treatment, but not at 600 mM, while Methanosaetaceae were significantly inhited at 300 mM NaCl treatment, but not at 600 mM. The taxonomic shifts in the total mRNA transcript pool corresponded well to the relative abundance changes of the microbial gene expressions. Clostridial transcripts affiliated with the categories 'DNA replication','DNA repair','protein folding', 'central carbohydrate metabolism' , and 'fermentaion' were significantly enriched in response to salt stress. In contrast, transcripts of Methanosarcinaceae related to the key metabolic pathway (methanogenesis) and protein folding were highly enriched with salt stress, but not 'DNA replication','DNA repair'. Among typical stress response categories, Clostridiaceae showed a strong transcriptional response related to “osmotic stress”, while transcripts of Methanosarcinaceae were highly overrepresented in “heat shock”. Generally, salt stress triggered a selective gene expressions of the paddy soil model system.