Deep Groundwater Evolution at Outokumpu, Eastern Finland : From Meteoric Water to Saline Gas-Rich Fluid

Within Precambrian continental shields, saline, gas-rich groundwaters are found in all over the world from bedrock fractures and pore spaces in the upper crust. Several processes, from seawater evaporation or freezing followed by infiltration to water rock interaction, have been suggested to be responsible for the characteristic features of these waters. In addition to reactions between water and the bedrock, active microbial communities inhabiting these waters, i.e. the deep biosphere, may play a significant role in shaping their surroundings by biogeochemical reactions, especially by contributing to the deep carbon cycle. The origin and evolution of deep groundwater in the 2.5 km deep Outokumpu Deep Drill Hole in eastern Finland was investigated using geochemical and isotopic methods. The sample material included water and gas derived from the drill hole by tube sampling, pumping and pressurized methods, as well as fracture minerals. Similar results were obtained for water samples using different sampling techniques. However, as uncontrolled degassing took place during tube sampling and pumping, it is suggested that pressurized methods should be used for gas sampling. Five water types were discerned along the drill hole, which reflect changes in lithology and indicate isolation from the surface and from each other within the Outokumpu bedrock. An evolutionary model was proposed that includes precipitation and infiltration of meteoric water at warmer than present climatic conditions, a shift in the stable isotopic composition of water and an increase in salinity through water rock interaction between virtually stagnant groundwater and the bedrock, and both the abiotic and biotic formation of hydrocarbons. Two independent lines of evidence from water stable isotopes and the accumulation of radiogenic and nucleogenic noble gases indicated isolation of the Outokumpu Deep Drill Hole groundwaters from the meteoric water cycle from the Eocene-Miocene epochs, placing the evolutionary model in the time frame of millions to tens of millions of years. The results shed light on how deep groundwaters have evolved in geochemical and microbiological processes through time and space. Furthermore, they emphasise the complexity of these environments, as they are being increasingly utilised for underground construction, and provide background information for assessment of the long-term safety of nuclear waste disposal.Suolaisia ja kaasupitoisia pohjavesiä tavataan ympäri maailmaa vanhoilla peruskallioalueilla. Koostumukseltaan ne eroavat selvästi merivedestä ja makeista pohja- sekä pintavesistä ja esiintyvät yleensä syvällä kallioperän raoissa ja huokosissa. Kallioperän lisääntyvä käyttö muun muassa kalliorakentamisessa, ydinjätteiden loppusijoituspaikkana, kaivostoiminnassa ja geoenergian tuotannossa tarkoittaa, että suolaisiin kalliopohjavesiin törmätään yhä useammin ja siten myös tiedon tarve näistä ympäristöistä on jatkuvasti kasvanut. Syvien kalliopohjavesien kehityksestä on esitetty useita toisistaan poikkeavia malleja. Lisäksi syvissä pohjavesissä elävien mikrobiyhteisöjen merkitystä ympäristönsä muokkaajina tunnetaan vielä huonosti. Tässä väitöstyössä tutkittiin syvien kalliopohjavesien alkuperää ja kehitystä Itä-Suomessa, Outokummussa sijaitsevasta, 2,5 km syvästä kairareiästä käyttäen geokemiaan ja isotooppeihin perustuvia menetelmiä. Vesi- ja kaasunäytteet otettiin reiästä käyttäen letkunäytteenottoa, pumppausta sekä paineellisena. Näistä paineellisten menetelmien osoitettiin soveltuvan kaasujen tutkimukseen parhaiten. Lisäksi tutkittiin kallion rakopinnoille kiteytyneitä mineraaleja. Tulosten perusteella Outokummun syväreiän pohjavesi voidaan jakaa viiteen vesityyppiin, joiden koostumus heijastelee kivilajien vaihtelua ja osoittaa vesien kehittyneen eristyksissä sekä toisistaan että maan pinnalta. Syvien pohjavesien kehityksestä laadittiin malli, joka käsittää veden suotautumisen kallioon nykyistä lämpimämmän ilmaston vallitessa, veden koostumuksen muutoksen ja suolapitoisuuden kasvun kivi-vesi - vuorovaikutuksen seurauksena, sekä hiilivetyjen muodostumisen geologisissa ja mikrobiologisissa prosesseissa. Veden isotooppikoostumukseen sekä jalokaasujen kertymiseen perustuvat, toisistaan riippumattomat menetelmät osoittivat, että Outokummun syväreiän vesi on ollut erillään maan pinnan vesikierrosta eoseeni-mioseenikausilta lähtien, keskimäärin 30 miljoonan vuoden ajan. Tulokset valaisevat syvien kalliopohjavesien ajallista ja paikallista kehitystä geokemiallisten ja mikrobiologisten prosessien tuloksena. Syvien pohjavesisysteemien monimutkaisuus tulee ottaa huomioon, kun kallioperää hyödynnetään. Tulokset tarjoavat tärkeää taustatietoa myös ydinjätteiden loppusijoituksen pitkäaikaisturvallisuuden arviointiin

The origin, source, and cycling of methane in deep crystalline rock biosphere

RK would like to thank the Finnish Research Program on Nuclear Waste Management (grants SALAMI and RENGAS) for funding.The emerging interest in using stable bedrock formations for industrial purposes, e.g., nuclear waste disposal, has increased the need for understanding microbiological and geochemical processes in deep crystalline rock environments, including the carbon cycle. Considering the origin and evolution of life on Earth, these environments may also serve as windows to the past. Various geological, chemical, and biological processes can influence the deep carbon cycle. Conditions of CH4 formation, available substrates and time scales can be drastically different from surface environments. This paper reviews the origin, source, and cycling of methane in deep terrestrial crystalline bedrock with an emphasis on microbiology. In addition to potential formation pathways of CH4, microbial consumption of CH4 is also discussed. Recent studies on the origin of CH4 in continental bedrock environments have shown that the traditional separation of biotic and abiotic CH4 by the isotopic composition can be misleading in substrate-limited environments, such as the deep crystalline bedrock. Despite of similarities between Precambrian continental sites in Fennoscandia, South Africa and North America, where deep methane cycling has been studied, common physicochemical properties which could explain the variation in the amount of CH4 and presence or absence of CH4 cycling microbes were not found. However, based on their preferred carbon metabolism, methanogenic microbes appeared to have similar spatial distribution among the different sites.Publisher PDFPeer reviewe

Implications of a short carbon pulse on biofilm formation on mica schist in microcosms with deep crystalline bedrock groundwater

Microbial life in the deep subsurface occupies rock surfaces as attached communities and biofilms. Previously, epilithic Fennoscandian deep subsurface bacterial communities were shown to host genetic potential, especially for heterotrophy and sulfur cycling. Acetate, methane, and methanol link multiple biogeochemical pathways and thus represent an important carbon and energy source for microorganisms in the deep subsurface. In this study, we examined further how a short pulse of low-molecular-weight carbon compounds impacts the formation and structure of sessile microbial communities on mica schist surfaces over an incubation period of similar to 3.5 years in microcosms containing deep subsurface groundwater from the depth of 500 m, from Outokumpu, Finland. The marker gene copy counts in the water and rock phases were estimated with qPCR, which showed that bacteria dominated the mica schist communities with a relatively high proportion of epilithic sulfate-reducing bacteria in all microcosms. The dominant bacterial phyla in the microcosms were Proteobacteria, Firmicutes, and Actinobacteria, whereas most fungal genera belonged to Ascomycota and Basidiomycota. Dissimilarities between planktic and sessile rock surface microbial communities were observed, and the supplied carbon substrates led to variations in the bacterial community composition.Peer reviewe

Rapid Reactivation of Deep Subsurface Microbes in the Presence of C-1 Compounds

Microorganisms in the deep biosphere are believed to conduct little metabolic activity due to low nutrient availability in these environments. However, destructive penetration to long-isolated bedrock environments during construction of underground waste repositories can lead to increased nutrient availability and potentially affect the long-term stability of the repository systems, Here, we studied how microorganisms present in fracture fluid from a depth of 500 m in Outokumpu, Finland, respond to simple carbon compounds (C-1 compounds) in the presence or absence of sulphate as an electron acceptor. C-1 compounds such as methane and methanol are important intermediates in the deep subsurface carbon cycle, and electron acceptors such as sulphate are critical components of oxidation processes. Fracture fluid samples were incubated in vitro with either methane or methanol in the presence or absence of sulphate as an electron acceptor. Metabolic response was measured by staining the microbial cells with fluorescent dyes that indicate metabolic activity and transcriptional response with RT-qPCR. Our results show that deep subsurface microbes exist in dormant states but rapidly reactivate their transcription and respiration systems in the presence of C-1 substrates, particularly methane. Microbial activity was further enhanced by the addition of sulphate as an electron acceptor. Sulphate- and nitrate-reducing microbes were particularly responsive to the addition of C-1 compounds and sulphate. These taxa are common in deep biosphere environments and may be affected by conditions disturbed by bedrock intrusion, as from drilling and excavation for long-term storage of hazardous waste.Peer reviewe

Rock Surface Fungi in Deep Continental Biosphere—Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap

Fungi have an important role in nutrient cycling in most ecosystems on Earth, yet their ecology and functionality in deep continental subsurface remain unknown. Here, we report the first observations of active fungal colonization of mica schist in the deep continental biosphere and the ability of deep subsurface fungi to attach to rock surfaces under in situ conditions in groundwater at 500 and 967 m depth in Precambrian bedrock. We present an in situ subsurface biofilm trap, designed to reveal sessile microbial communities on rock surface in deep continental groundwater, using Outokumpu Deep Drill Hole, in eastern Finland, as a test site. The observed fungal phyla in Outokumpu subsurface were Basidiomycota, Ascomycota, and Mortierellomycota. In addition, significant proportion of the community represented unclassified Fungi. Sessile fungal communities on mica schist surfaces differed from the planktic fungal communities. The main bacterial phyla were Firmicutes, Proteobacteria, and Actinobacteriota. Biofilm formation on rock surfaces is a slow process and our results indicate that fungal and bacterial communities dominate the early surface attachment process, when pristine mineral surfaces are exposed to deep subsurface ecosystems. Various fungi showed statistically significant cross-kingdom correlation with both thiosulfate and sulfate reducing bacteria, e.g., SRB2 with fungi Debaryomyces hansenii

Rock Surface Fungi in Deep Continental Biosphere—Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap

Fungi have an important role in nutrient cycling in most ecosystems on Earth, yet their ecology and functionality in deep continental subsurface remain unknown. Here, we report the first observations of active fungal colonization of mica schist in the deep continental biosphere and the ability of deep subsurface fungi to attach to rock surfaces under in situ conditions in groundwater at 500 and 967 m depth in Precambrian bedrock. We present an in situ subsurface biofilm trap, designed to reveal sessile microbial communities on rock surface in deep continental groundwater, using Outokumpu Deep Drill Hole, in eastern Finland, as a test site. The observed fungal phyla in Outokumpu subsurface were Basidiomycota, Ascomycota, and Mortierellomycota. In addition, significant proportion of the community represented unclassified Fungi. Sessile fungal communities on mica schist surfaces differed from the planktic fungal communities. The main bacterial phyla were Firmicutes, Proteobacteria, and Actinobacteriota. Biofilm formation on rock surfaces is a slow process and our results indicate that fungal and bacterial communities dominate the early surface attachment process, when pristine mineral surfaces are exposed to deep subsurface ecosystems. Various fungi showed statistically significant cross-kingdom correlation with both thiosulfate and sulfate reducing bacteria, e.g., SRB2 with fungi Debaryomyces hansenii

Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids

The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from groundwater of six fracture zones from 180 to 2300aEuro-m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related operational taxonomic units (OTUs) form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteriaceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed possible "keystone" genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found in oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found in other deep Precambrian terrestrial bedrock environments.Peer reviewe

What the Flux? – Water-Rock-Microbe Interactions and Crustal Gases in the Deep Subsurface

The deep, dark fracture zones of the continental crust host a fascinating interplay between water, rocks, and microbes, resulting in the production and consumption of gases, including methane, volatile organic compounds (VOCs), and hydrogen. Various geological factors influence the formation and release of these crustal gases, including the local rock type with its concentration of radioactive elements and carbon, temperature, and the connectivity and dynamics of fracture systems with each other and to the surface.To understand the formation, accumulation, and release of crustal gases, methodologies of hydrogeochemistry, biogeochemistry, and isotope geochemistry can be employed. Sample collection from drill holes and mines, coupled with on-line monitoring of gas flux rate and composition, provides important data. Furthermore, the integration of molecular biological methods enhances our understanding of the water-rock-microbe interactions that shape the deep subsurface gas realm.Crustal gases have crucial implications for life in extreme environments, including those outside of our planet Earth, but potentially also pose significant challenges to drilling, mining, and their environmental impact. Moreover, crustal gases hold relevance for the energy sector, contributing to both the long-term safety of geological disposal of nuclear waste, carbon footprint of geothermal wells, and the exploration of hydrogen as a sustainable energy resource

The origin, source, and cycling of methane in deep crystalline rock biosphere

The emerging interest in using stable bedrock formations for industrial purposes, e.g. nuclear waste disposal, has increased the need for understanding microbiological and geochemical processes in deep crystalline rock environments, including the carbon cycle. Considering the origin and evolution of life on Earth, these environments may also serve as windows to the past. Various geological, chemical and biological processes can influence the deep carbon cycle. Conditions of CH4 formation, available substrates and time scales can be drastically different from surface environments. This paper reviews the origin, source and cycling of methane in deep terrestrial crystalline bedrock with an emphasis on microbiology. In addition to potential formation pathways of CH4, microbial consumption of CH4 is also discussed. Recent studies on the origin of CH4 in continental bedrock environments have shown that the traditional separation of biotic and abiotic CH4 by the isotopic composition can be misleading in substrate-limited environments, such as the deep crystalline bedrock. Despite of similarities between Precambrian continental sites in Fennoscandia, South Africa and North America, where deep methane cycling has been studied, common physicochemical properties which could explain the variation in the amount of CH4 and presence or absence of CH4 cycling microbes were not found. However, based on their preferred carbon metabolism, methanogenic microbes appeared to have similar spatial distribution among the different sites

Dissolved Microbial Methane in the Deep Crystalline Crust Fluids–Current Knowledge and Future Prospects

Methane is a powerful greenhouse gas, of which most is produced by microorganisms in a process called methanogenesis. One environment where methanogenic microorganisms occur is the deep biosphere. The deep biosphere environment comprises a variety of ecosystem settings; marine habitats such as subseafloor sediments, rock pore volumes within subseafloor basalts, and terrestrial settings such as sedimentary rocks and crystalline bedrock fracture networks. Microbial methane formed in these environments influence the biological, chemical, and geological cycles of the upper crust, and may seep out of the deep into the atmosphere. This review focuses on the process of microbial methanogenesis and methane oxidation in the relatively underexplored deep crystalline-bedrock hosted subsurface, as several works in recent years have shown that microbial production and consumption occur in this energy-poor rock-fracture-hosted environment. These recent findings are summarized along with techniques to study the source and origins of methane in the terrestrial crust. Future prospects for exploration of these processes are proposed to combine geochemical and microbial techniques to determine whether microbial methanogenesis is a ubiquitous phenomenon in the crystalline crust across space and time. This will aid in determining whether microbial methane in the globally vast deep rock-hosted biosphere environment is a significant contributor to the global methane reservoir