Transcriptomic response of soil crust microbiota to hydration

Drylands are considered the largest terrestrial biome on Earth and are characterized by low water availability, combined with high UV irradiation, heat and osmotic stress. Biological soil crusts (BSCs) are highly adapted microbial surface communities common in drylands, and represent an ideal model systems to study physiological survival mechanisms and resuscitation dynamics of dryland soil microbiota. We investigated the immediate, short-term resuscitation of BSC microbial community members upon a controlled, simulated rain event at the bulk, population and single-cell level. In-situ metatranscriptomics combined with metagenome-assembled genomes (PRJEB36534) allowed us to track the transcriptional responses of individual microbial populations during the rain event. This was complemented by quantifying anabolically active cells at the single-cell level via heavy water incubations followed by the analysis of deuterium incorporation into biomass with nanoscale secondary ion mass-spectrometry. Our study revealed a rapid and collective resuscitation of the taxonomically and physiologically diverse microbiota, which was characterized by distinct resuscitation phases. In the first 30 minutes, most populations generated energy, putatively from degradation of storage compounds, and repaired DNA, before continuing with their main metabolic functions. In several populations, energy generation was supported phototrophically or by oxidizing atmospheric gases, both during hydrated and dry periods. We further identified key anti-oxidative proteins important for desiccation survival such as Mn-based catalase and rubrerythrin. This metabolic flexibility and functional diversity enabled about 90% of the cells to reactivate within 12 hours. Estimated generation times confirm that rain events can provide a window for cell division and thus maintenance of population sizes.