Microbiome composition and geochemical characteristics of deep subsurface high-pressure environment, Pyhäsalmi mine Finland.

Hanna Miettinen,Merja Itävaara,Mikko Numminen,Riikka Kietäväinen,Elina Sohlberg,Lasse Ahonen

doi:10.3389/fmicb.2015.01203

Hanna Miettinen, Merja Itävaara + Show 4 more

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https://doi.org/10.3389/fmicb.2015.01203

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Abstract

Pyhäsalmi mine in central Finland provides an excellent opportunity to study microbial and geochemical processes in a deep subsurface crystalline rock environment through near-vertical drill holes that reach to a depth of more than two kilometers below the surface. However, microbial sampling was challenging in this high-pressure environment. Nucleic acid yields obtained were extremely low when compared to the cell counts detected (1.4 × 104 cells mL−1) in water. The water for nucleic acid analysis went through high decompression (60–130 bar) during sampling, whereas water samples for detection of cell counts by microscopy could be collected with slow decompression. No clear cells could be identified in water that went through high decompression. The high-pressure decompression may have damaged part of the cells and the nucleic acids escaped through the filter. The microbial diversity was analyzed from two drill holes by pyrosequencing amplicons of the bacterial and archaeal 16S rRNA genes and from the fungal ITS regions from both DNA and RNA fractions. The identified prokaryotic diversity was low, dominated by Firmicute, Beta- and Gammaproteobacteria species that are common in deep subsurface environments. The archaeal diversity consisted mainly of Methanobacteriales. Ascomycota dominated the fungal diversity and fungi were discovered to be active and to produce ribosomes in the deep oligotrophic biosphere. The deep fluids from the Pyhäsalmi mine shared several features with other deep Precambrian continental subsurface environments including saline, Ca-dominated water and stable isotope compositions positioning left from the meteoric water line. The dissolved gas phase was dominated by nitrogen but the gas composition clearly differed from that of atmospheric air. Despite carbon-poor conditions indicated by the lack of carbon-rich fracture fillings and only minor amounts of dissolved carbon detected in formation waters, some methane was found in the drill holes. No dramatic differences in gas compositions were observed between different gas sampling methods tested. For simple characterization of gas composition the most convenient way to collect samples is from free flowing fluid. However, compared to a pressurized method a relative decrease in the least soluble gases may appear.

Highlights

Microbial life has been observed in deep subsurface continental bedrock fractures and aquifers despite the harsh conditions in terms of energy, nutrients, pressure, and space
Deep fluids from the Pyhäsalmi mine have several features in common with other deep Precambrian continental subsurface environments (e.g., Nurmi et al, 1988; Frape et al, 2003): they are saline, Ca-dominated and have water stable isotope compositions left from the meteoric water line
The microbial high-pressure sampling succeeded only partially as the amount of prokaryotic DNA/RNA collected was especially low. This was probably due to the highpressure decompression that may have damaged part of the cells and the nucleic acids likely have passed through the filter

Summary

Introduction

Microbial life has been observed in deep subsurface continental bedrock fractures and aquifers despite the harsh conditions in terms of energy, nutrients, pressure, and space. In a fractured rock environment, rock itself may provide a nutritional and energetic substrate to sustain minimal metabolic activity (Fredrickson and Balkwill, 2006). Microbial cells in these settings catabolize 104–106 fold more slowly than model organisms in nutrient-rich cultures and subsist with energy fluxes that are 1000-fold lower than the typical culture-based estimates of maintenance requirements (Hoehler and Jørgensen, 2013). The dominant bacterial and archaeal groups in different deep subsurface bedrock environments vary based on prevailing lithology and hydrogeochemistry (Nyyssönen et al, 2014; Bomberg et al, 2015). Fungal communities are suggested to be active in continental and deep subseafloor sediments (Edgcomb et al, 2010; Orsi et al, 2013), and recently, evidence of rich and active fungal communities were found in continental crystalline bedrock facture zones (Sohlberg et al, 2015)

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