Epilithic microbial communities and their functionality in the deep continental bedrock

There is a knowledge gap regarding the microbes attaching to the deep bedrock surfaces and their interactions with minerals. This thesis work characterized bacterial, fungal, and archaeal communities in the mica schist surface biofilms and in the deep groundwater from the depths of 500 and 967 m in the Outokumpu bedrock in Finland. An in-situ biofilm sampler was designed that enabled enrichment of microbes on mica schist surfaces in-situ within the deep subsurface. The attachment process of the deep groundwater microbial communities was followed in similar manner in microcosms. Long-term effects of a low molecular weight carbon compound pulse (methane, methanol, acetate) on evolving microbial communities on the mica schist and in the water phase was assessed.

Different microbial morphologies were observed on the mica schist surfaces, such as rods, cocci, spirilli and long microbial filaments. Sessile microbes were shown to produce slimy extracellular polymeric substances (EPS), different attachment related surface appendices as well as tubular structures between cells. Most of the surface attached microbes represented single cells or small colonies, but also more dense biofilm structures were observed. Mineral heterogenicity could lead to uneven distribution of microbial cells on mica schist surface.

Epilithic microbial communities on the mica schist generally differed from planktic groundwater communities. Microbial cells attached to both mica schist and glass surfaces, and the communities differed depending on the material. Distinct microbial community developed on mica schist in the in-situ conditions of Outokumpu bedrock in comparison to the mica schist communities developed in the longer enrichments in the laboratory microcosms. After in-situ enrichment in the deep bedrock conditions, mica schist surfaces hosted a diverse fungal community, containing e.g., yeasts adapted to extreme conditions and fungi belonging to the Mortierella-genus. In addition, microcosms also enriched filamentous fungi such as Penicillium and Aspergillus. The fungal community size is generally smaller than that of bacterial communities in the deep groundwaters and mica schist surfaces. Even though deep biosphere is known to host fungi, the actions and role of fungi are not well understood. The fungal communities were versatile and rich, which indicates how well adapted they are to bedrock environment.

Genes linked to heterotrophy as well as to the cycling of carbon and sulfur were common in the metagenome assembled genomes (MAGs) of the rock surface attached bacteria. Sulfate reducing bacteria (SRB) attached especially to the mica schist surfaces, which could act as a carbon or sulfur source for the microbes. Mica schist enriched in-situ in the Outokumpu deep drill hole contained various SRB and thiosulfate utilizing bacteria. Genes encoding enzymes needed in the degradation of complex compounds were common across the bacterial groups. This implies the important role of both necromass degradation and recycling in sustaining the deep life.