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

Abstract

<jats:title>Summary</jats:title><jats:p>Microbial communities play essential roles in the biosphere and understanding the mechanisms underlying their functional adaptations to environmental conditions is critical for predicting their behavior. 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 of 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 very different levels of total transcriptional activity and that different metabolic pathways were activated in their transcriptomes. We report that a novel <jats:italic>Dolichomastix</jats:italic> alga – the only eukaryote found in this system – was by far the most active community member. It produced the vast majority of the community’s photosynthetic transcripts despite being outnumbered by members of the <jats:italic>Cyanobacteria</jats:italic>. The divergence in the transcriptional landscapes of these segregated communities, compared to 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.</jats:p><jats:sec><jats:title>Originality-Significance Statement</jats:title><jats:p>While the metagenomics of hypersaline environments have already led to many discoveries, the transcriptional adaptations and functions of halophilic microbial communities in natural environments remains understudied. We perform the first robust meta-omic investigation of a hypersaline desert ecosystem, linking the genomic and transcriptional elements of the community. Our analysis unexpectedly revealed that Eukaryotes may be the main primary producers in this extreme environment, despite halophilic Archaea and Bacteria dominating the biomass. We also expand on the existing known diversity of halophilic viruses and demonstrate abundance (copies per million reads) and metatranscriptomic activity (transcripts per million reads); putative hosts are shown on the right.</jats:p></jats:sec>

Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil

“…Viruses have also been studied in hypersaline Atacama environments; Crits-Christoph et al (29) identified viral sequences and their potential hosts in halite endoliths. Additionally, Uritskiy et al (30) detected transcriptionally active viruses potentially infecting Halobacteria also inhabiting halite salt nodules in a salar located in the Atacama Desert. These niche halite host-virus relationships highlight the need to characterize the impact of viruses in broad desert soils that represent one of the largest and rapidly expanding terrestrial ecosystems on the planet (~35% of the Earth's land surface (31)).…”

Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community

“…We obtained 10 to 100 ng of RNA/g of grounded halite. RT-PCR was used to validate the absence of contaminating DNA in the total RNA used for RNA-seq libraries with 16S rRNA primers 515F/926R (18).…”

“…Whole-genome sequencing libraries were prepared using the KAPA HyperPlus kit (Roche) as previously described (14) and sequenced with paired 150-bp reads on the HiSeq 2000 platform at the Johns Hopkins Genetic Resources Core Facility (GRCF). Total RNA-seq libraries were prepared with the SMARTer Stranded RNA-seq kit (38), using 25 ng of RNA input and 12 cycles for library amplification, as previously described (18). We sequenced 21 libraries from replicate samples from 2016 and 24 libraries from replicate samples from 2017 (see Table S1 in the supplemental material).…”

“…Total RNA extracted from environmental samples and enrichment cultures was converted into cDNA using the SuperScript III first-strand synthesis system (Thermo Fisher) using 5 ng of input RNA. The cDNA was then amplified using 515F/926R 16S rRNA primers as previously described (18). Amplicons were sequenced using Sanger sequencing (GENEWIZ).…”

“…Such a community inhabits halite (salt) nodules in Salars of the Atacama Desert, Chile, which is one of the oldest and driest deserts on Earth (16,17). The halite endolithic (within rock) community harbors mostly members of the Archaea (Halobacteria), unique Cyanobacteria, diverse heterotrophic bacteria, and a novel type of algae (16,17), all of which were shown to be transcriptionally active (18). The main source of liquid water for this community is from salt deliquescence (19), and it is sustained by CO 2 fixed via photosynthesis (16,20).…”