Rock surface attaching deep biosphere microbes and their functionality

Finnish deep bedrock and groundwaters create a niche that hosts diverse microbial life. Life in the deep is considered extreme as microbes face elevated pressure, absolute darkness, high salinity as well as low nutrient and carbon concentrations. Deep groundwater microbiomes have been studied in depth compared to the microbial communities residing on bedrock surfaces due to for example sampling technical issues. Now we characterized sessile mica schist microbial communities originating from the deep biosphere of Outokumpu, Finland (Nuppunen-Puputti et al., 2021; 2022; 2023).
Deep biosphere rock surface biofilms were studied both through in-situ incubations in the scientific deep drill hole in Outokumpu at the depths of 500 m and 967 m, and with microcosm experiments in the laboratory conditions. Microbial communities were characterized with amplicon sequencing of bacteria, fungi, and archaea. Rock surface community functionality was studied through metagenomics, and microbial marker gene copy counts were estimated with qPCR. Rock surface biofilms were visualized with scanning electron microscopy (SEM).
Rocky metagenomes hosted genes for heterotrophic metabolism, sulfur and carbon cycling as well as arsenate and selenate reduction. In addition, low molecular weight carbon compounds were shown to affect the structure of formed biofilms communities. A variety of genes linked to degradation of complex compounds were detected in the rock surface metagenomes suggesting potential for efficient recycling of necromass in deep subsurface biofilms. Sulfate reducing bacteria (SRB) were common on mica schist surfaces indicating that rocks could act a source of sulfur for deep subsurface microbes. SEM of mica schist surfaces showed that microbial cells had various attachment strategies linked to production of extracellular polymeric substances (EPS), long tubular or hair-like structures and stalks.

References
Nuppunen-Puputti M, Kietäväinen R, Purkamo, L, Rajala, P, Itävaara M, Kukkonen I & Bomberg M (2021) Rock surface fungi in deep continental biosphere – exploration of microbial community formation with subsurface in-situ biofilm trap. Microorganisms, 29:9(1): E64. Nuppunen-Puputti M, Kietäväinen R, Raulio M, Soro A, Purkamo L, Kukkonen I & Bomberg M (2022) Epilithic microbial community
functionality in deep oligotrophic continental bedrock. Frontiers in Microbiology, 13: 82048.
Nuppunen-Puputti M, Kietäväinen R, Kukkonen I & Bomberg M (2023) Implications of a short carbon pulse on biofilm formation in
microcosms with deep crystalline bedrock groundwater. Frontiers in Microbiology, 14:1054084.