Viable and active microorganisms in the deep terrestrial biosphere

Although the continental deep biosphere is estimated to contain 2 to 19% of the earth’s total biomass, it is still one of the least understood ecosystems on the planet. A key question for the terrestrial deep biosphere is the viability and activity of the large diversity of microorganisms present. This work shows that the microbial populations in aquifers with different chemistry and depth below the surface are viable and active and their diversity decreased with depth below the surface. Quantitative PCR and high throughput 16S rRNA gene sequencing revealed no significant differences in 16S rRNA gene abundances and microbial diversity between total and viable communities. This suggested that the populations were adapted to the prevailing oligotrophic conditions and that non-viable cells are rapidly degraded and recycled into new biomass. In addition, in situ fixed RNA transcripts aligned to the three domains of life, supporting activity within these communities. Many of the SSU rRNA transcripts grouped within recently described candidate phyla or could not be mapped to known branches on the tree of life, suggesting that a large portion of the active biota in the deep biosphere remains unexplored. Despite the extremely oligotrophic conditions, mRNA transcripts revealed a diverse range of metabolic strategies carried out by different taxa. These results emphasize the need to further investigate microbial activities in the deep biosphere and the importance of unclassified and candidate phyla in this environment.