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Collecting water samples in the Pyhäsalmi mine. (a) Collection of mine water dripping from the roof at the depth of 240 m belowground (sample P240m), (b) collection of water sample from the pond at depth 500 m belowground (sample P500m), and (c-d) sampling point at depth 600 m belowground (sample P600m).
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Microbial communities of iron-rich water in the Pyhäsalmi mine, Finland, were investigated with high-throughput amplicon sequencing and qPCR targeting bacteria, archaea, and fungi. In addition, the abundance of Leptospirillum and Acidithiobacillus was assessed with genus-specific qPCR assays, and enrichment cultures targeting aerobic ferrous iron o...
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Acid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from16S rRNA gene amplicons but...
Citations
... Another suggested source of H 2 for methanogenesis comes from fungi [22,60]. Anaerobic fungi can degrade refractory material, and the presence of fungi has been found in multiple sites across the deep Fennoscandian bedrock [61][62][63]. Fossilized remnants of intergrown fungal hyphae with substantially 13 C-enriched calcite suggest a close syntrophic relationship between anaerobic fungi and methanogens in the deep biosphere [22]. Fungi may thus contribute substrates for microbial methanogenesis in deep continental bedrock by degrading organic matter. ...
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.
... The typical bacterial number in river waters can reach 10 6 to 10 7 cells/ml [5]. Acidic mine waters were shown to contain higher diversity as microbial numbers reach 106-10 7 16S rRNA gene copies/ml [6]. Escherichia coli (E.coli) is a water-borne bacteria. ...
Escherichia coli as water-borne bacteria exists in the recirculation water of coal flotation and affects the recovery of coal flotation. In order to study the effect of Escherichia coli on coal flotation, we changed the concentration of Escherichia coli and pH in the coal flotation system and found that Escherichia coli had an adverse effect on coal flotation. The concentration of Escherichia coli was negatively correlated with the recovery of coal. When the concentration of Escherichia coli reached 5.0 × 10 ⁹ cells/ml, the recovery of coal flotation was 50.25%, and the change of pH basically did not affect the adverse effect of Escherichia coli on coal flotation. The mechanism was studied through Zeta potential, Fourier transform infrared spectroscopy, Scanning electron microscopy and Contact angle measurements. The results revealed that Escherichia coli could be adsorbed to the coal surface by hydrogen bonding, which changed the hydrophobicity of the coal surface and then reduced the recovery of coal flotation.
... In contrast to Äspö, the Pyhäsalmi mine in Finland is seated in Paleoproterozoic volcanogenic massive sulfides, where the lower mine stratigraphy is composed of felsic, tuffaceous volcanites and the upper mine is seated in mafic lavas, breccias, and pyroclastics (Miettinen et al., 2015). Bomberg et al. (2019) explored fracture waters in the upper mine, between 240-600 m depth using enrichments (focusing on iron based metabolisms) coupled with taxonomic diversity analysis, following up on a previous study by Kay et al. (2014). At these depths, the freshly exposed surfaces allow oxidation of the host rock, weathering the minerals and impacting the fracture fluids. ...
... On the whole, the community has generally and historically made the assumptions that, (1) when methane or hydrogen gas are measurable in subsurface fluids, the biosphere is likely dominated by sulfate reduction and methanogenesis, and (2) presence of heterotrophic metabolisms indicates influence from the surface biosphere. These assumptions made a great deal of sense several decades ago, but have been consistently shown to be less relevant in many locations as more data are acquired, reduced sulfur species, ammonium, ferrous iron and other metals are shown to be important sources of electrons, and abiotic reactions resulting in synthesis of organic carbon are known to provide fuel for biomass synthesis (Amend and Teske, 2005;McCollom et al., 2010;Shock and Canovas, 2010;Osburn et al., 2014;Bomberg et al., 2019). Very recent considerations of the structure of the energetic landscape in deep continental biosphere settings have begun to paint a picture that methanogenesis may be limited at greater depths, or more prevalent where fresh groundwater mixes with deeper fluids (e.g., Osburn et al., 2014;Leong and Shock, 2020). ...
The subsurface is one of the last remaining ‘uncharted territories’ of Earth and is now accepted as a biosphere in its own right, at least as critical to Earth systems as the surface biosphere. The terrestrial deep biosphere is connected through a thin veneer of Earth’s crust to the surface biosphere, and many subsurface biosphere ecosystems are impacted by surface topography, climate, and near surface groundwater movement and represent a transition zone (at least ephemerally). Delving below this transition zone, we can examine how microbial metabolic functions define a deep terrestrial subsurface. This review provides a survey of the most recent advances in discovering the functional and genomic diversity of the terrestrial subsurface biosphere, how microbes interact with minerals and obtain energy and carbon in the subsurface, and considers adaptations to the presented environmental extremes. We highlight the deepest subsurface studies in deep mines, deep laboratories, and boreholes in crystalline and altered host rock lithologies, with a focus on advances in understanding ecosystem functions in a holistic manner.
... Recently, AUMs have been recognised as promising model sites for basic microbiology research, proving that the scientific value of AUMs is not limited to local geology, environmental impacts, and history of mining. Conversely, an increasing amount of microbiology research in AUMs covers topics of general importance: microbial speciation patterns, diversity, relations of community structure and geochemical redox windows, microbial genomics, proteomics, and complex structure of microbial biofilms (e.g., Denef et al., 2010;Bomberg et al., 2019;Osburn et al., 2014;2019;Ullrich et al., 2016;Ziegler et al., 2013). In contrast, studies revealing new strains of universally common bacteria or purely descriptive metabarcoding analyses are routinely performed in caves (e.g., Turrini et al., 2020;Morse et al., 2021). ...
... The microbiota of mines are variable and depend mostly on the redox windows that supply the microbial consortia with energy (Osburn et al., 2014;2019). Within each trophic system, various microbial consortia alternate depending on the physicochemical properties of each microhabitat (e.g., Bomberg et al., 2019). As a result, no "typical mine microbiome" can be determined. ...
We have investigated a typical abandoned underground slate mine situated in the Bohemian Massif (Central Europe) in order to describe its elementary components and to outline the varied relations among them. Based on the results from geological, geomorphological, hydrological, microclimatic, and biological investigation, we have defined the abandoned underground mine as an important but overlooked semi-natural ecosystem that represents an azonal and relatively fast evolving environment. Unlike any other studies published so far, we have found it also vulnerable in terms of fragility and time-limited stability. Our results together with a comprehensive discussion highlight the fundamental features of the abandoned underground mine and finally serve as a basis on which we introduce a conceptual model of the abandoned underground mine. The complex and interdisciplinary perception of abandoned underground mines is crucial for appropriate environmental assessment, tourist management, natural protection or remediation.
... This drainage leads to deterioration of the surface water quality in the mining area and affects the regional ecological environment and the mining of high-quality coal. Previous studies on pyrite and acid drainage mainly focused on the genetic characteristics of pyrite [2][3][4][5], the genetic mechanism of acid mine drainage [6,7], the treatment of acid mine drainage [8][9][10][11], and the temporal effect of mine water on aquatic environments [12][13][14][15]. However, the main controlling factors of the formation process of acid mine drainage and its influence threshold remain unclear. ...
The discharge of acidic water has become an environmental issue of great concern worldwide. In order to investigate the characteristics and mechanism of acidic water induced by pyrite in sulfur-rich mines, indoor static precipitation and dynamic leaching simulation experiments were carried out under the conditions of pyrite content, rock particle size, media combination, and ambient temperature. At the same time, this paper used the gray correlation method to quantitatively analyze the influencing factors. The results showed that the degree of groundwater acidification was negatively correlated with the rock particle size and temperature and positively correlated with the pyrite content. The quantitative analysis of the effect of each factor on acid mine drainage pH was pyrite content > temperature > rock size. When considering different media conditions, the combined effect of the three media on reducing the acidification degree of mine water was limestone > gangue > coal. In addition, dynamic leaching and static soaking have different effects on the acidification of the mine water, with the latter acidifying more rapidly. It is also concluded that although pyrite enrichment was the main controlling factor affecting the acidification of mine water in nature, complexation of trivalent iron ions adsorbed in the formation was more likely to be the main causal mechanism for the rapid acidification of mine water in coal mining areas.
... Acidophilic iron and sulphur oxidizing microorganisms are frequently found in oligotrophic, acidic environments with high concentrations of dissolved iron and sulphur [7][8][9]. Such environments may be found in and around mines, where sulphidic ore has been exposed to oxygen and water and a natural dissolution of the rock leads to the release of sulphuric acid, which further dissolves the rock resulting in acid rock drainage. ...
Blasting and fracking of rock in mines exposes fresh rock surfaces to the local water and microbial communities. This may lead to leaching of metals from the rock by chemical or biological means and can cause acidification of the water system in the mine, i.e., acid rock drainage (ARD). Failure to prevent leakage of metal contaminated mine water may be harmful for the environment, especially to the local groundwater. In the Rudna mine, Poland, an in situ bioleaching pilot test at approximately 1 km depth was performed in the H2020 BIOMOre project (Grant Agreement #642456). After the leaching stage, different methods for irreversible inhibition of acidophilic iron oxidizing microorganisms used for reoxidation of reduced iron in the leaching solution were tested and were shown to be effective. However, the potential of the natural mine water microbial communities to cause leaching of copper or acidification of the mine waters has not been tested. In this study, we set up a microcosm experiment simulating the exposure of freshly fractionated Kupferschiefer sandstone or black schist to two different chloride-rich water types in the Rudna mine. The pH of the microcosms water was measured over time. At the end of an 18-week incubation, the bacterial community was examined by high throughput sequencing and qPCR, and the presence of copper tolerant heterotrophic bacteria was tested by cultivation. The dissolution of copper into the chloride rich microcosm water was measured. The pH in the microcosms did not decrease over the time of incubation. The sandstone increased the number of bacteria in the microcosms with one or over two orders of magnitude compared to the original water. The bacterial communities in the two tested mine waters were diverse and similar despite the difference in salinity. The bacterial diversity was high but changed in the less saline water during the incubation. There was a high content of sulphate reducing bacteria in the original mine waters and in the microcosms, and their number increased during the incubation. No acidophilic iron oxidizers were detected, but in the microcosms containing the less saline water low numbers of Cu tolerant bacteria were detected. Copper to a concentration of up to 939 mg L−1 was leached from the rock also in the microbe-free negative controls, which was up to 2.4 times that leached in the biotic microcosms, indicating that the leaching was also abiotic, not only caused by bacteria.
... Bacteroides bacteria are isolated mainly in an anaerobic environment, such as anaerobic digestion of sludge and intestinal tract contents. Proteobacteria bacteria are derived mainly from anaerobic digestion of sludge and manure [32,33], consistent with the result of pig manure as a substrate in this study. Studies have found that Firmicutes and Bacteroidetes are the main microflora in the hydrolysis process during anaerobic digestion, Proteobacteria, Chloroflexi, Firmicutes and Bacteroidetes are the main flora in the acidification process, and these microorganisms play important roles in the anaerobic digestion of organic waste [34]. ...
Anaerobic digestion can be inhibited at low temperatures in cold regions. This study investigated the effects of fermentation temperature, total solids (TS) concentration and stirring speed on swine manure biogas production by anaerobic fermentation experiments based on the quadratic regression orthogonal rotation combination method. The results showed that the fermentation temperature and TS had significant effects on swine manure biogas production rates. The theoretical and experimental amounts of gas production at the optimal process parameters were 2857.46 mL and 2820.0 mL, respectively. Methanobacteria and Methanomicrobia were the main methane-producing genera for samples in six different anaerobic digestion phases , with relative abundances of 2.25 to 5.59% and 0.85 to 3.02%, respectively. The acetotrophic bacterium Methanosaeta was absolutely dominant, attributable to acetic acid metabolic pathways occurring more easily at low temperatures and Methanosaeta was more competitive when the acetic acid concentration was in the range of 38.8 to 252.2 mg L⁻¹.
... Many microorganisms can be found in AMD, and this biodiversity is justified by the wide range of pH, temperature, and oxygen content in AMD from site to site [7][8][9]. ...
Acid mine drainage (AMD) is a common environmental problem in many sulphide mines worldwide, and it is widely accepted that the microbial community plays a major role in keeping the process of acid generation active. The aim of this work is to describe, for the first time, the microbial community thriving in goethite and jarosite Fe precipitates from the AMD of the Libiola mine. The observed association is dominated by Proteobacteria (>50%), followed by Bacteroidetes (22.75%), Actinobacteria (7.13%), Acidobacteria (5.79%), Firmicutes (2.56%), and Nitrospirae (1.88%). Primary producers seem to be limited to macroalgae, with chemiolithotrophic strains being almost absent. A phylogenetic analysis of bacterial sequences highlighted the presence of heterotrophic bacteria, including genera actively involved in the AMD Fe cycle and genera (such as Cytophaga and Flavobacterium) that are able to reduce cellulose. The Fe precipitates constitute a microaerobic and complex environment in which many ecological niches are present, as proved by the wide range of bacterial species observed. This study is the first attempt to quantitatively characterize the microbial community of the studied area and constitutes a starting point to learn more about the microorganisms thriving in the AMD of the Libiola mine, as well as their potential applications.
... Detailed reports of AMD origin and different processes contributing to AMD generation, including the role of ironand/or sulfur-oxidizing microbes are available in literature (Baker and Banfield, 2003;Hallberg, 2010;Chen et al., 2016). In many AMD sites, oxidation is primarily catalyzed by naturally occurring bacteria called Acidithiobacillus ferrooxidans (Chen et al., 2015;Mesa et al., 2017;Bomberg et al., 2019;Wang et al., 2019b) and these bacteria accelerate the oxidation reactions for sulfides of most HM (Akcil and Koldas, 2006). According to Edwards et al. (2000), about 75% of AMD produced results from microbial activity. ...
Environmental degradation related to mining-generated acid mine drainage (AMD) is a major global concern, contaminating surface and groundwater sources, including agricultural land. In the last two decades, many developing countries are expanding agricultural productivity in mine-impacted soils to meet food demand for their rapidly growing population. Further, the practice of AMD water (treated or untreated) irrigated agriculture is on the increase, particularly in water-stressed nations around the world. For sustainable agricultural production systems, optimal microbial diversity, and functioning is critical for soil health and plant productivity. Thus, this review presents up-to-date knowledge on the microbial structure and functional dynamics of AMD habitats and AMD-impacted agricultural soils. The long-term effects of AMD water such as soil acidification, heavy metals (HM), iron and sulfate pollution, greatly reduces microbial biomass, richness, and diversity, impairing soil health plant growth and productivity, and impacts food safety negatively. Despite these drawbacks, AMD-impacted habitats are unique ecological niches for novel acidophilic, HM, and sulfate-adapted microbial phylotypes that might be beneficial to optimal plant growth and productivity and bioremediation of polluted agricultural soils. This review has also highlighted the impact active and passive treatment technologies on AMD microbial diversity, further extending the discussion on the interrelated microbial diversity, and beneficial functions such as metal bioremediation, acidity neutralization, symbiotic rhizomicrobiome assembly, and plant growth promotion, sulfates/iron reduction, and biogeochemical N and C recycling under AMD-impacted environment. The significance of sulfur-reducing bacteria (SRB), iron-oxidizing bacteria (FeOB), and plant growth promoting rhizobacteria (PGPRs) as key players in many passive and active systems dedicated to bioremediation and microbe-assisted phytoremediation is also elucidated and discussed. Finally, new perspectives on the need for future studies, integrating meta-omics and process engineering on AMD-impacted microbiomes, key to designing and optimizing of robust active and passive bioremediation of AMD-water before application to agricultural production is proposed.
... The acidic ferruginous model Lake 77 provides ideal conditions to investigate the extent to which Fe(II) oxidation linked autotrophy (chemolithoautotrophy) contributes to the biological carbon pump versus the contribution from classical photoautotrophy. The Fe-cycling microbes found in Lake 77 mimic the previously characterized AMD and pit lake microbial communities [64,65]. Our molecular data consistently show the dominance of autotrophic FeOB (Leptospirillum and Ferrovum) in iron snow, whereas autotrophic communities in marine or lake snow are dominated by phytoplankton (i.e., cyanobacteria and algae). ...
Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO2 fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace 13CO2 incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6–85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. 13CO2 incorporation studies identified active chemolithoautotroph Ferrovum under both conditions. Only 1.0–5.3% relative 13C abundances were found in heterotrophic Acidiphilium and Acidocella under oxic conditions. These data show that iron oxidizers play an important role in CO2 fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.
