The combination of advances in DNA sequencing technologies and sampling in numerous locales around the world is changing our understanding of the deep biosphere. A dramatically enhanced appreciation for diversity goes hand in hand with a realization of common keystone species in subsurface niches.
In a new study from DCO Deep Life and Deep Energy scientists, Lotta Purkamo (VTT Technical Research Center, Finland) and colleagues investigate the microbes living in the Outokumpu deep borehole in Finland . The borehole extends over 2km into the Fennoscandian Precambrian shield, with fractures into the rock along the length of the hole allowing the team to assess microbial diversity as a function of depth.
By sequencing 16S ribosomal RNA from biomass isolated from the borehole, Purkamo et al were able to describe microbes thriving at six different depths; 180, 500, 967, 1820, 2260, and 2300 meters. While the team did not obtain full metagenomes, they used an in silico method for predicting the microbial metagenomes of the fractures in which a program (PICRUSt) compares 16S sequences with public databases of full genomes. At shallower depths, the team found bacterial species with genomes suggesting physiological versatility and the ability to utilize multiple metabolic pathways. Bacteria with unknown metabolisms were more common in the deeper fractures. However, in all samples, the majority of bacterial species were members of the so-called rare, or dark, biosphere.
When analyzing archaeal genomes, the authors found that the deepest fracture fluids hosted numerous SAGMEG species. These Archaea were recently reclassified as Hadesarchaea, a new lineage of deep microbes found ubiquitously in both deep terrestrial and marine systems.
"The deep subsurface as a habitat is harsh and demanding,” said Purkamo. “Maybe because of the arduous environmental conditions, microbial communities in the deep subsurface around the world share features. Hydrogen-oxidising Comamonadaceae and Dethiobacter colonize crystalline bedrock fracture fluids in Outokumpu, but also hydrothermal vents, alkaline springs, and subterrestrial aquifers. As well as Hadesarchaea, other methanogens have been found at many deep subsurface sites.”
Serpentinization and and Fischer-Tropsch type reactions produce organic carbon, and may support the whole ecosystem in Outokumpu. Many of the detected phylotypes affiliate with heterotrophic microbes with a capacity for hydrogen oxidation. These microbes may well rely on energy and organic carbon from abiotic sources.
“As it was evident for Outokumpu fractures in this paper, microbial dark matter forms a majority of the microbial communities especially in the deepest depths,” added Purkamo. “More studies are needed to identify and to understand the physiology and functionality of this rare biosphere."
Images: Top left: The Outokumpu borehole in Finland. Credit: Leea Ojala, VTT. Middle right: Co-author Maija Nuppunen-Puputti analyzes samples from the borehole. Credit: Pauliina Rajala, VTT.