Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community

Summary Microbial communities play essential roles in the biosphere and understanding the mechanisms underlying their functional adaptations to environmental conditions is critical for predicting their behaviour. This aspect of microbiome function has not been well characterized in natural high‐salt environments. To address this knowledge gap, and to build a general framework relating the genomic and transcriptomic components in a microbiome, we performed a meta‐omic survey of extremophile communities inhabiting halite (salt) nodules in the Atacama Desert. We found that the major phyla of this halophilic community have different levels of total transcriptional activity, at the selected time‐points, and that different metabolic pathways were activated in their transcriptomes. We report that a novel Dolichomastix alga—the only eukaryote found in this system—was the most active community member. It produced the vast majority of the community's photosynthetic transcripts despite being outnumbered by Cyanobacteria. The divergence in the transcriptional landscapes of these segregated communities, compared with the relatively stable metagenomic functional potential, suggests that microbiomes in each salt nodule undergo unique transcriptional adjustments to adapt to local conditions. We also report the characterization of several previously unknown halophilic viruses, many of which exhibit transcriptional activity indicative of host infection.