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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.

The deep terrestrial biosphere hosts vast sessile rock surface communities and biofilms, but thus far, mostly planktic communities have been studied. We enriched deep subsurface microbial communities on mica schist in microcosms containing bedrock groundwater from the depth of 500 m from Outokumpu, Finland. The biofilms were visualized using scanning electron microscopy, revealing numerous different microbial cell morphologies and attachment strategies on the mica schist surface, e.g., bacteria with outer membrane vesicle-like structures, hair-like extracellular extensions, and long tubular cell structures expanding over hundreds of micrometers over mica schist surfaces. Bacterial communities were analyzed with amplicon sequencing showing that Pseudomonas, Desulfosporosinus, Hydrogenophaga, and Brevundimonas genera dominated communities after 8-40 months of incubation. A total of 21 metagenome assembled genomes from sessile rock surface metagenomes identified genes involved in biofilm formation, as well as a wide variety of metabolic traits indicating a high degree of environmental adaptivity to oligotrophic environment and potential for shifting between multiple energy or carbon sources. In addition, we detected ubiquitous organic carbon oxidation and capacity for arsenate and selenate reduction within our rocky MAGs. Our results agree with the previously suggested interaction between the deep subsurface microbial communities and the rock surfaces, and that this interaction could be crucial for sustaining life in the harsh anoxic and oligotrophic deep subsurface of crystalline bedrock environment.

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.

Estimation of archaeal numbers by use of fluorescent DNA binding dyes is challenging, because primers targeting the archaeal 16SrRNA genes readily also bind to bacterial 16S rRNA gene sequences, especially when the relative abundance of bacteria is greater than that of archaea. In order to increase specificity, we optimized a fluorescent probe-based assay using previously published archaeal primers and probe. The assay was tested on genomic DNA of pure bacterial and archaeal cultures and optimized using PCR amplicons of the archaeal pure cultures. The used bacterial strains showed slight amplification using the fluorescent dye assay, whereas all archaeal strains could be amplified with the archaea primers used. Due to differences in genome size and number of 16S rRNA gene copies between the tested archaeal strains, the amplification level varied greatly between the strains. Therefore, we also tested the amplification using PCR amplified fragments of the archaeal 16S rRNA genes. The tests with the archaeal 16S rRNA gene amplicons showed good amplification, although the amplification efficiency still varied between archaeal strains. The qPCR assay was used to estimate the archaeal numbers in process water of a multi-metal mine's metallurgical plant [1] and will be used in similar future microbiological analysis included in the H2020 ITERAMS project (Grant agreement# 730480).

Spent nuclear fuel will be deposited in deep geological repositories in the crystalline bedrock in Finland and Sweden. The repositories rely on the multi-barrier KBS-3 concept, where the first barriers consist of copper-sheeted cast-iron canisters that contain the spent nuclear fuel rods. However, the repositories will be influenced by both abiotic and biotic factors. The repositories, when closed, will be flooded with a mixture of both the local groundwater and surface water and eventually return to an anoxic deep subsurface environment. This environment will contain microbial communities that utilize chemical components that have been produced both abiotically and biologically, which will determine the composition and size of the microbial communities in the repositories. Overtime, integrity of the storage canisters may become compromised due to, for example, microbially influenced corrosion, which may result from the corrosive nature of hydrogen sulfide produced in biological sulfate reduction. Radionuclides originating from the decay of the spent nuclear fuel may escape into the repository environment, from where they may diffuse further into the surface environment. In this chapter, we aim to shed light on some of the most important aspects of the Fennoscandian Shield deep crystalline bedrock biosphere identified to date, with examples of putative biogeochemical cycles that prevail in these environments.

openaire: EC/H2020/730480/EU//ITERAMS The changes in water quality owing to recirculation of water in mineral processing plants can compromise the plant performance as well as maintenance needs. Therefore, mining process water quality assessment is becoming critical. Nevertheless, very few studies have investigated the suitability of the current analysis methodology practiced in certified laboratories for evaluating mining process water quality. This article presents two case studies to highlight the major issues encountered when performing sampling for physicochemical and chemical parameters in process water at two European mine sites using procedures from two certified laboratories. In addition, microorganisms were shown to be abundant in process waters and likely affect the mining water chemistries. However, the protocols used for microbial studies are not optimal for mining process samples, and need to be improved. The results showed difficulties in providing satisfactory results when analyzing control samples. Additionally, the analysis results presented a strong imbalance in TDS and sulfur compounds. Several potential causes associated with the poor quality of the analysis results have been outlined with a specific focus on the preservation methods. A literature review on the degradation of thiosalts suggested that the current preservation procedures are not suitable for preserving sulfur compounds. Moreover, the results indicated that the water matrix strongly influenced the validity of the chosen analysis method. In conclusion, the analysis methods should be customized for the different mining water matrix types in order to ensure the accuracy and reproducibility of the results.

Microorganisms enter the flotation process mainly from intake water and ore material. The diversity and number of microorganisms can vary significantly from mine to mine. In flotation, the conditions including oxygen levels, temperature, and nutrients from ore, intake water, and reagents are often favorable for the microbial growth. The mining industry aims to close the water loops, which is expected to result in the accumulation of microorganisms in the process waters with potential effects on flotation performance. Bioflotation, bioleaching, and bio-oxidation have been studied for decades as tools for concentrating and dissolving minerals. In contrast, there is limited scientific literature or industrial knowledge about microorganisms that naturally inhabit and prevail in minerals processing applications over a wide pH range. Microorganisms affect minerals when they selectively attach to the surfaces, produce extracellular polymeric substances (EPS) and polysaccharides, oxidize or reduce the minerals, change the pH and Eh of the process solution, and degrade organic flotation chemicals. Microorganisms contain different structural components that affect their surface chemistry, charge, and behavior in flotation, but these properties may also change via adaptation and solution conditions. Almost all studies on flotation have focused on chemical and physical parameters, and the role of naturally occurring microorganisms has remained underexplored. Advances in genomics and proteomics offer possibilities to describe not only which microorganisms are present, but also which physiological functions are being exercised. This article reviews the current knowledge of microorganisms in various mineral processes, identifies potential microbe–mineral interactions in flotation, describes the gaps in current knowledge, and concludes with the potential effects of microorganisms on flotation, especially in closed water loops.

By whichever means we explore Earth from its surface, the information gained about our planet’s interior is always indirect, a model put together using multiple types of evidence. Drilling is the only way to verify such models against reality. However, drilling and retrieving samples and data is costly, complex, and sometimes dangerous - this is exactly where the International Continental Scientic Drilling Program (ICDP) comes in. The goal of the ICDP is to encourage Earth scientists to use the investigative tool of scientic drilling to test models from information gathered at the Earth’s surface. Given the typically high cost of drilling and of research in boreholes, it is clear that any proposals for drilling with ICDP’s help must address substantial scientific questions with a strong focus on societal needs. This Science Plan lays out some of the most important issues that ICDP aims to investigate over the next decade. The key questions address fundamental science, but many also link to wider societal challenges encompassed in the United Nations Sustainable Development Goals (SDGs). In particular, ICDP projects can provide important information to underpin the SDGs related to clean water and sanitation, affordable and clean energy, sustainable cities and communities, and climate action.