Regulatory non-coding small RNAs are diverse and abundant in an extremophilic microbial community

Abstract

Regulatory small RNAs (sRNAs) represent a major class of regulatory molecules that play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been primarily investigated in a few model organisms and little is known about the dynamics of sRNA synthesis in natural environments, and the roles of these short transcripts at the community level. Analyzing the metatranscriptome of a model extremophilic community inhabiting halite nodules (salt rocks) from the Atacama Desert with SnapT - a new sRNA annotation pipeline - we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs. The halite sRNAs were taxonomically diverse with the majority expressed by members of the Halobacteria. We found asRNAs with expression levels negatively correlated with that of their putative overlapping target, suggesting a potential gene regulatory mechanism. A number of itsRNAs were conserved and significantly differentially expressed (FDR<5%) between 2 sampling time points allowing for stable secondary structure modeling and target prediction. This work demonstrates that metatranscriptomic field experiments link environmental variation with changes in RNA pools and have the potential to provide new insights into environmental sensing and responses in natural microbial communities through non-coding RNA mediated gene regulation.