Microorganisms and Minerals in Natural and Engineered Environments

A special issue of Minerals (ISSN 2075-163X). This special issue belongs to the section "Environmental Mineralogy and Biogeochemistry".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 26381

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Guest Editor
Laboratory of Chemolithotrophic Microorganisms, Russian Academy of Sciences, Leninsky Ave, 33, bld. 2, 119071 Moscow, Russia
Interests: biomining; sulfur and iron cycles; sulfide ores and ore concentrates; bioleaching; microbial diversity; acidophilic microorganisms; heavy metal resistance, stress response and metabolism of acidophiles
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Guest Editor
Winogradsky Institute of Microbiology, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia
Interests: bioleaching; biooxidation; hydrometallurgy; chemolithotrophic acidophiles; waste biotreatment
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue focuses on minerals and microorganisms from natural and engineered systems, such as acidic hot springs and soils, volcanic areas, mineral deposits, mining sites, and acid mine drainage. We invite you to share your recent studies on mineral processes and microorganisms involved in them, as well as microbe–mineral interactions. We also welcome contributions reporting on microbial diversity, metabolism, resistance, and stress response, which are of interest for basic and applied science, including, but not limited to, biohydrometallurgy, applied microbiology, and mineral chemistry. Studies of (bio)leaching and (bio)oxidation of sulfidic minerals are especially encouraged.

Dr. Anna Panyushkina
Dr. Maxim Muravyov
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Minerals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Mineral processing
  • Microbial mineralogy
  • Biohydrometallurgy
  • Microorganisms
  • Leaching and oxidation of sulfide raw materials
  • Acidophiles
  • Microbial diversity
  • Mineral deposits
  • Metal mining activities
  • Volcanic areas and hydrothermal vents
  • Acid mine drainage (AMD)
  • Metal(loid)s
  • Microbial resistance and stress response

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Published Papers (10 papers)

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Research

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11 pages, 5521 KiB  
Article
A Case of Predominance of Alicyclobacillus tolerans in Microbial Community during Bioleaching of Pentlandite-Chalcopyrite Concentrate
by Anna Panyushkina, Maxim Muravyov and Natalya Fomchenko
Minerals 2022, 12(4), 396; https://doi.org/10.3390/min12040396 - 23 Mar 2022
Cited by 5 | Viewed by 1586
Abstract
Bacterial isolates assigned to the species Alicyclobacillus tolerans, which occupies an intermediate position between an organotrophic genus Alicyclobacillus and mixotrophic genus Sulfobacillus, were revealed as members of the acidophilic chemolithotrophic community during stirred-tank bioleaching of violarite–pentlandite–chalcopyrite concentrate at 40 °C. Surprisingly, [...] Read more.
Bacterial isolates assigned to the species Alicyclobacillus tolerans, which occupies an intermediate position between an organotrophic genus Alicyclobacillus and mixotrophic genus Sulfobacillus, were revealed as members of the acidophilic chemolithotrophic community during stirred-tank bioleaching of violarite–pentlandite–chalcopyrite concentrate at 40 °C. Surprisingly, this species succeeded more common iron-oxidizing community members after a series of bioleaching processes in bioreactors. The possibility of mixotrophic and organoheterotrophic growth of Al. tolerans, tolerance to low pH values (1.0–1.15), as well as preservation of cells via sporulation under unfavorable conditions, may explain its key role in the bioleaching of the copper–nickel bulk concentrate. Isolation of two other sulfur-oxidizing pure cultures dominating the microbial community, together with their phylogenetic characterization, allowed the assignment of these isolates to the species Acidithiobacillus caldus. This and other studies of acidophilic microbial communities are important for the development and intensification of the bioleaching processes, including a biobeneficiation approach previously proposed by us. Full article
(This article belongs to the Special Issue Microorganisms and Minerals in Natural and Engineered Environments)
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16 pages, 3574 KiB  
Article
Non-Ferrous Metals and PGM Recovery from Low-Grade Copper–Nickel Concentrate by Bioleaching and Further Cyanidation
by Elena Latyuk, Vitaliy Melamud, Anatoly Lavrinenko, Dmitriy Makarov and Aleksandr Bulaev
Minerals 2022, 12(3), 340; https://doi.org/10.3390/min12030340 - 10 Mar 2022
Cited by 4 | Viewed by 2996
Abstract
The aim of the present work was to perform copper, nickel, and platinum group metals (PGMs) recovery from low-grade copper–nickel concentrate containing pyrrhotite, pentlandite, and chalcopyrite by bioleaching in stirred tank reactors in batch mode and subsequent cyanidation. The concentrate contained (%) Fe [...] Read more.
The aim of the present work was to perform copper, nickel, and platinum group metals (PGMs) recovery from low-grade copper–nickel concentrate containing pyrrhotite, pentlandite, and chalcopyrite by bioleaching in stirred tank reactors in batch mode and subsequent cyanidation. The concentrate contained (%) Fe 32.7, Cu 0.7, Ni 2.3, Stotal 20.9, Ssulfide 17, 0.1 g/t Pt, and 1.35 g/t Pd. The bioleaching was performed at 30 and 40 °C using two different microbial consortia. At 30 °C, bioleaching was performed using mixed culture including Acidithiobacillus ferrivorans strains isolated from the sample of acid mine drainage from copper–nickel deposit. At 40 °C, bioleaching was performed using microbial population formed during long-term bioleaching of copper-zinc concentrate at 40 °C. Bioleaching was performed for 40 days at pulp density of 10% (solid to liquid ratio 1:10). At 30 °C, 70% Ni and 14% Cu were leached, while 72% Ni and 34% Cu were recovered in the solution at 40 °C. PGM were extracted from the concentrate and bioleaching residue obtained at 40 °C by cyanidation. Cyanidation made it possible to extract 5.5% Pt and 17.3% Pd from the concentrate and 37.8% Pt and 87.8% Pd from the bioleaching residue. Thus, it was shown that the concentrate studied might be processed using bioleaching and subsequent cyanidation to extract both non-ferrous metals and PGM. Full article
(This article belongs to the Special Issue Microorganisms and Minerals in Natural and Engineered Environments)
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13 pages, 3847 KiB  
Article
Reaction of Microorganisms to Long-Term Waste Reclamation of Soil Degraded by the Sulfur Mining Industry
by Jolanta Joniec, Grażyna Żukowska, Marta Bik-Małodzińska, Edyta Kwiatkowska and Kamila Rojek
Minerals 2021, 11(11), 1226; https://doi.org/10.3390/min11111226 - 04 Nov 2021
Cited by 5 | Viewed by 1664
Abstract
The research was carried out to assess soil condition many years after waste introduction for reclamation purposes. The parameters of the activity of soil microorganisms responsible for the revitalization processes in degraded soils were used in the research. Soil material was derived from [...] Read more.
The research was carried out to assess soil condition many years after waste introduction for reclamation purposes. The parameters of the activity of soil microorganisms responsible for the revitalization processes in degraded soils were used in the research. Soil material was derived from the area of the former sulfur mine. The results showed that even a single waste introduction to degraded soil caused long-lasting effects in the activity of soil microorganisms. The most favorable changes were caused by the addition of sewage sludge and the use of mineral wool in the form of a pad. The application of lime alone turned out to be the least beneficial for the revitalization processes, i.e., restoring the homeostasis of biological life in degraded soil. This research is a continuation of study that concerned the initial recultivation period. The obtained research results show the need for monitoring soils reclaimed with waste, not only in the initial period but also in the following years. These results allow evaluation of the usefulness of the parameters of soil microbial activity in monitoring soil environments subjected to strong human pressure. The results can be used to assess the risks associated with the introduction of waste into the environment. Full article
(This article belongs to the Special Issue Microorganisms and Minerals in Natural and Engineered Environments)
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20 pages, 18721 KiB  
Article
Cyanobacterial Communities of Carbonate Sediments and Biomineralization in Peterhof Fountains’ Water Supply System, Russia
by Oksana A. Rodina, Oleg S. Vereshchagin, Dmitry Yu. Vlasov, Marina S. Zelenskaya, Dmitrii V. Pankin, Nikita V. Mitrofanov, Michael Yu. Nikitin, Kseniia Yu. Vasileva and Olga V. Frank-Kamenetskaya
Minerals 2021, 11(11), 1199; https://doi.org/10.3390/min11111199 - 28 Oct 2021
Cited by 1 | Viewed by 2147
Abstract
The role of cyanobacterial communities in the formation of carbonate sediments (ancient and modern) is not completely clear. We studied the cyanobacterial communities connected with carbonate sediments of the freshwater bodies feeding the historical Peterhof fountains (Saint-Petersburg, Russia). Cyanobacterial communities were studied by [...] Read more.
The role of cyanobacterial communities in the formation of carbonate sediments (ancient and modern) is not completely clear. We studied the cyanobacterial communities connected with carbonate sediments of the freshwater bodies feeding the historical Peterhof fountains (Saint-Petersburg, Russia). Cyanobacterial communities were studied by metagenome analysis and optical microscopy. Carbonates associated with cyanobacterial communities (both in situ and in vitro) were studied by powder X-ray diffraction analysis, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and Raman spectroscopy. The interconnection between the mineral composition of carbonate sediments and inhabiting microorganism species was established. The leading role of cyanobacteria in carbonate biomineralization in fresh water of Peterhof fountains water supply system was shown. Cyanobacteria of 24 genera were revealed in sediments composed of calcite and aragonite. The crystallization of carbonates on the surface of 13 species of cyanobacteria was found. Using model experiments, a significant contribution of cyanobacterial species of the Oscillatoriaceae family (Phormidium spp., Lyngbya sp., Oscillatoria formosa) to carbonate biomineralization is demonstrated. Full article
(This article belongs to the Special Issue Microorganisms and Minerals in Natural and Engineered Environments)
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16 pages, 3380 KiB  
Article
The Potential Role of S-and Fe-Cycling Bacteria on the Formation of Fe-Bearing Mineral (Pyrite and Vivianite) in Alluvial Sediments from the Upper Chicamocha River Basin, Colombia
by Claudia Patricia Quevedo, Juan Jiménez-Millán, Gabriel Ricardo Cifuentes, Antonio Gálvez, José Castellanos-Rozo and Rosario Jiménez-Espinosa
Minerals 2021, 11(10), 1148; https://doi.org/10.3390/min11101148 - 18 Oct 2021
Cited by 3 | Viewed by 2190
Abstract
S- and Fe-cycling bacteria can decisively affect the crystallization of Fe-bearing minerals in sediments from fluvial environments. We have studied the relationships between the Fe-bearing mineral assemblage and the bacterial community composition in the sediments rich in organic matter from the upper Chicamocha [...] Read more.
S- and Fe-cycling bacteria can decisively affect the crystallization of Fe-bearing minerals in sediments from fluvial environments. We have studied the relationships between the Fe-bearing mineral assemblage and the bacterial community composition in the sediments rich in organic matter from the upper Chicamocha river basin (Colombia). Rapid flowing sections of the river contain sediments that have a high redox potential, are poor in organic matter and are enriched in kaolinite and quartz. On the other hand, the mineral assemblage of the sediments deposited in the La Playa dam with a high content in organic matter is enriched in Fe-bearing minerals: (a) vivianite and pyrite in the permanently flooded sediments of the dam and (b) pyrite and goethite in the periodically emerged sediments. The bacterial community composition of these sediments reveals anthropic organic matter pollution processes and biodegradation associated with eutrophication. Moreover, periodically emerged sediments in the La Playa dam contain bacterial groups adapted to the alternation of dry and wet periods under oxic or anoxic conditions. Cell-shaped aggregates with a pyritic composition suggest that sulfate-reducing bacteria (SRB) communities were involved in the precipitation of Fe-sulfides. The precipitation of vivianite in the flooded sediments was favored by a greater availability of Fe(II), which promoted the iron-reducing bacteria (IRB) enrichment of the sediments. The presence of sulfur-oxidizing bacteria (SOB) in the flooded sediments and the activity of iron-oxidizing bacteria (IOB) in the periodically emerged sediments favored both pyrite crystallization under a high sulfide availability and the oxidation of microbially precipitated monosulfides. Moreover, IOB enhanced goethite formation in the periodically emerged sediments. Full article
(This article belongs to the Special Issue Microorganisms and Minerals in Natural and Engineered Environments)
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25 pages, 6425 KiB  
Article
Microbe-Mediated Mn Oxidation—A Proposed Model of Mineral Formation
by Susanne Sjöberg, Changxun Yu, Courtney W. Stairs, Bert Allard, Rolf Hallberg, Sara Henriksson, Mats Åström and Christophe Dupraz
Minerals 2021, 11(10), 1146; https://doi.org/10.3390/min11101146 - 18 Oct 2021
Cited by 7 | Viewed by 2566
Abstract
Manganese oxides occur in a wide range of environmental settings either as coatings on rocks, sediment, and soil particles, or as discrete grains. Although the production of biologically mediated Mn oxides is well established, relatively little is known about microbial-specific strategies for utilizing [...] Read more.
Manganese oxides occur in a wide range of environmental settings either as coatings on rocks, sediment, and soil particles, or as discrete grains. Although the production of biologically mediated Mn oxides is well established, relatively little is known about microbial-specific strategies for utilizing Mn in the environment and how these affect the morphology, structure, and chemistry of associated mineralizations. Defining such strategies and characterizing the associated mineral properties would contribute to a better understanding of their impact on the local environment and possibly facilitate evaluation of biogenicity in recent and past Mn accumulations. Here, we supplement field data from a Mn rock wall deposit in the Ytterby mine, Sweden, with data retrieved from culturing Mn oxidizers isolated from this site. Microscopic and spectroscopic techniques are used to characterize field site products and Mn precipitates generated by four isolated bacteria (Hydrogenophaga sp., Pedobacter sp., Rhizobium sp., and Nevskia sp.) and one fungal-bacterial co-culture (Cladosporium sp.—Hydrogenophaga sp. Rhizobium sp.—Nevskia sp.). Two of the isolates (Pedobacter sp. and Nevskia sp.) are previously unknown Mn oxidizers. At the field site, the onset of Mn oxide mineralization typically occurs in areas associated with globular wad-like particles and microbial traces. The particles serve as building blocks in the majority of the microstructures, either forming the base for further growth into laminated dendrites-botryoids or added as components to an existing structure. The most common nanoscale structures are networks of Mn oxide sheets structurally related to birnessite. The sheets are typically constructed of very few layers and elongated along the octahedral chains. In places, the sheets bend and curl under to give a scroll-like appearance. Culturing experiments show that growth conditions (biofilm or planktonic) affect the ability to oxidize Mn and that taxonomic affiliation influences crystallite size, structure, and average oxidation state as well as the onset location of Mn precipitation. Full article
(This article belongs to the Special Issue Microorganisms and Minerals in Natural and Engineered Environments)
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11 pages, 1199 KiB  
Article
16S rRNA Gene-Based Profiling of the Microbial Community in an Acid Mine Drainage Fe Precipitate at Libiola Mine (Liguria, Italy)
by Sirio Consani, Stefano Ghignone, Marina Pozzolini, Marco Giovine, Luigi Vezzulli and Cristina Carbone
Minerals 2021, 11(10), 1064; https://doi.org/10.3390/min11101064 - 29 Sep 2021
Cited by 1 | Viewed by 1675
Abstract
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, [...] Read more.
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. Full article
(This article belongs to the Special Issue Microorganisms and Minerals in Natural and Engineered Environments)
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19 pages, 5868 KiB  
Article
Metabolomic Profiling of Biolayers on the Surface of Marble in Nature and Urban Environment. Case Study of Karelia and St. Petersburg
by Katerina V. Sazanova, Marina S. Zelenskaya, Oksana A. Rodina, Alexey L. Shavarda and Dmitry Yu Vlasov
Minerals 2021, 11(10), 1033; https://doi.org/10.3390/min11101033 - 23 Sep 2021
Cited by 2 | Viewed by 1604
Abstract
The formation of biolayers of various taxonomic and biochemical composition occurs on the rock surfaces under various environmental conditions. The composition of metabolites in various types of biolayers on the marble surface in natural outcrops and urban environment was studied. Metabolome profiling was [...] Read more.
The formation of biolayers of various taxonomic and biochemical composition occurs on the rock surfaces under various environmental conditions. The composition of metabolites in various types of biolayers on the marble surface in natural outcrops and urban environment was studied. Metabolome profiling was fulfilled by GC-MS. It was found that communities in urban environment are much less biochemically diverse than in a quarry. The seasonal differences in metabolite network between samples dominate over taxonomic ones in biolayers with predomination of algae and cyanobacteria and in biolayers with predomination of fungi. The biolayers of different stage of soil formation are less susceptible to seasonal variability. Full article
(This article belongs to the Special Issue Microorganisms and Minerals in Natural and Engineered Environments)
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Review

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25 pages, 3249 KiB  
Review
The Role of Microorganisms in the Formation, Dissolution, and Transformation of Secondary Minerals in Mine Rock and Drainage: A Review
by Jose Eric Ortiz-Castillo, Mohamad Mirazimi, Maryam Mohammadi, Eben Dy and Wenying Liu
Minerals 2021, 11(12), 1349; https://doi.org/10.3390/min11121349 - 30 Nov 2021
Cited by 9 | Viewed by 4425
Abstract
Mine waste rock and drainage pose lasting environmental, social, and economic threats to the mining industry, regulatory agencies, and society as a whole. Mine drainage can be alkaline, neutral, moderately, or extremely acidic and contains significant levels of sulfate, dissolved iron, and, frequently, [...] Read more.
Mine waste rock and drainage pose lasting environmental, social, and economic threats to the mining industry, regulatory agencies, and society as a whole. Mine drainage can be alkaline, neutral, moderately, or extremely acidic and contains significant levels of sulfate, dissolved iron, and, frequently, a variety of heavy metals and metalloids, such as cadmium, lead, arsenic, and selenium. In acid neutralization by carbonate and silicate minerals, a range of secondary minerals can form and possibly scavenge these potentially harmful elements. Apart from the extensively studied microbial-facilitated sulfide oxidation, the diverse microbial communities present in mine rock and drainage may also participate in the formation, dissolution, and transformation of secondary minerals, influencing the mobilization of these metals and metalloids. This article reviews major microbial-mediated geochemical processes occurring in mine rock piles that affect drainage chemistry, with a focus on the role of microorganisms in the formation, dissolution, and transformation of secondary minerals. Understanding this is crucial for developing biologically-based measures to deal with contaminant release at the source, i.e., source control. Full article
(This article belongs to the Special Issue Microorganisms and Minerals in Natural and Engineered Environments)
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15 pages, 2641 KiB  
Review
Interaction between Microbes, Minerals, and Fluids in Deep-Sea Hydrothermal Systems
by Shamik Dasgupta, Xiaotong Peng and Kaiwen Ta
Minerals 2021, 11(12), 1324; https://doi.org/10.3390/min11121324 - 26 Nov 2021
Cited by 4 | Viewed by 3600
Abstract
The discovery of deep-sea hydrothermal vents in the late 1970s widened the limits of life and habitability. The mixing of oxidizing seawater and reduction of hydrothermal fluids create a chemical disequilibrium that is exploited by chemosynthetic bacteria and archaea to harness energy by [...] Read more.
The discovery of deep-sea hydrothermal vents in the late 1970s widened the limits of life and habitability. The mixing of oxidizing seawater and reduction of hydrothermal fluids create a chemical disequilibrium that is exploited by chemosynthetic bacteria and archaea to harness energy by converting inorganic carbon into organic biomass. Due to the rich variety of chemical sources and steep physico-chemical gradients, a large array of microorganisms thrive in these extreme environments, which includes but are not restricted to chemolithoautotrophs, heterotrophs, and mixotrophs. Past research has revealed the underlying relationship of these microbial communities with the subsurface geology and hydrothermal geochemistry. Endolithic microbial communities at the ocean floor catalyze a number of redox reactions through various metabolic activities. Hydrothermal chimneys harbor Fe-reducers, sulfur-reducers, sulfide and H2-oxidizers, methanogens, and heterotrophs that continuously interact with the basaltic, carbonate, or ultramafic basement rocks for energy-yielding reactions. Here, we briefly review the global deep-sea hydrothermal systems, microbial diversity, and microbe–mineral interactions therein to obtain in-depth knowledge of the biogeochemistry in such a unique and geologically critical subseafloor environment. Full article
(This article belongs to the Special Issue Microorganisms and Minerals in Natural and Engineered Environments)
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