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

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 14131

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Prof. Dr. Hiromi Konishi

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Department of Geology, Niigata University, Niigata 951-8510, Japan
Interests: biominerals; nanominerals; mineral defects; transmission electron microscopy
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Special Issue Information

Dear Colleagues,

Although it is well established that microorganisms play important roles in geological systems, the variety of microbial biomineralization, the function of microorganisms in the mineralization, and the mechanism of mineral formation require further investigation. Non-living organic substances, such as dead cells, also mediate mineral formation which is called organimineralization. How non-living organic substances are involved in mineral formation is not well understood. We focus on the variety of microbial biomineralization and organimineralization, structure, chemistry, and crystallography of biominerals, and the formation mechanism of microbial biominerals.

We are pleased to invite you to contribute your work to this Special Issue entitled “Microbial Biomineralization and Organimineralization”. In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following: (1) Microbially controlled or induced biomineralization; (2) Organimineralization which is mediated by organic substances, but not directly produced by living organisms; (3) Microbial reduction and oxidation; (4) Bioremediation; (5) Biomining; (6) Metal transformation and concentration in natural environments, and ore deposit by microorganisms; (7) Global biogeochemical cycling of elements; (8) Carbonate deposition and carbon sink; and (9) Biosynthesis of nanoparticles by microorganisms.

Prof. Dr. Hiromi Konishi
Guest Editor

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

biomineralization
organimineralization
bioremediation
biomining
biosynthesis
microbial oxidation and reduction
nanoparticles

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Published Papers (10 papers)

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Research

17 pages, 3552 KiB

Open AccessArticle

Formation of Core-Rim Magnetite with a Carbonaceous Core in Mid-Archean Banded Iron Formation from the Barberton Greenstone Belt, South Africa

by Tatsuro Manabe and Hiromi Konishi

Minerals 2025, 15(3), 218; https://doi.org/10.3390/min15030218 - 24 Feb 2025

Viewed by 540

Abstract

Through the analysis of core-rim magnetite, we demonstrate that the core contains carbonaceous materials (CMs) derived from a 3.2-billion-year-old banded iron formation within the Barberton Greenstone Belt in South Africa. Using scanning electron microscopy, energy-dispersive X-ray spectroscopy, and Raman spectroscopy, we establish a direct association between these CMs and the magnetite. Although the possibility that CMs formed from the hydrothermal decomposition of siderite cannot be ruled out, several lines of evidence indicate a likely microbial origin for the CMs. Firstly, Raman spectroscopy reveals that the CMs exhibit characteristics of low-maturity biogenic organic matter (OM) featuring aliphatic carbon chains, which supports the notion that organic carbon compounds mature during burial metamorphism at temperatures below approximately 200 °C. Secondly, phosphorus and sulfur detected in the CMs suggest a microbial origin. Lastly, the formation of the unique texture of core-rim magnetite can be conceptualized as follows: Fe²⁺ is oxidized through anoxygenic photosynthesis, leading to the precipitation of ferrihydrite. This ferrihydrite is then transformed into magnetite by iron-reducing microorganisms. Subsequently, the magnetite grows larger through oriented attachment, which also confines OM. Ultimately, smooth magnetite rims may have preserved the OM for up to 3.2 billion years. Full article

(This article belongs to the Special Issue Microbial Biomineralization and Organimineralization)

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17 pages, 2131 KiB

Open AccessArticle

Leveraging Biomineralization in Repurposed Stirred Reactors for Mn/Zn Removal from Mine Water: Insights from a Laboratory-Scale Study

by Fumiya Kurogi, Peiyu Liu and Naoko Okibe

Minerals 2025, 15(3), 211; https://doi.org/10.3390/min15030211 - 22 Feb 2025

Viewed by 563

Abstract

This study developed a semi-passive treatment system for manganese (Mn)- and zinc (Zn)-containing mine water by repurposing a neutralization tank into a biologically active stirred reactor. Laboratory-scale experiments demonstrated efficient removal of Mn²⁺ (>97%) and Zn²⁺ (>80%) with hydraulic retention times (HRTs) as short as 6 h—significantly faster than traditional passive systems. XRD and XANES analyses identified the predominant formation of birnessite, a layered Mn oxide, during Mn²⁺ oxidation, with Zn co-treatment promoting the precipitation of Zn-containing carbonates. Despite decreasing crystallinity of birnessite over time, microbial activity, dominated by Mn-oxidizing genera, such as Sphingomonas, Pseudonocardia, Sphingopyxis, Nitrospira, and Rhodobacter, persisted in the presence of Zn²⁺, ensuring system stability. Importantly, the low leachability of Mn and Zn from the resulting sludge in TCLP tests confirmed its environmental safety and potential for reuse. By leveraging existing infrastructure and microbial biomineralization, this system bridges the gap between passive and active treatments, significantly reducing treatment footprints and operational costs. These findings highlight the potential of repurposing mine water treatment tanks as a scalable, cost-effective solution for sustainable mine water remediation. Full article

(This article belongs to the Special Issue Microbial Biomineralization and Organimineralization)

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17 pages, 2741 KiB

Open AccessArticle

Leucophosphite and Associated Minerals in the Fossil Bat Guano Deposit in Gaura cu Muscă Cave, Locvei Mountains, Romania

by Delia-Georgeta Dumitraş and Ştefan Marincea

Minerals 2025, 15(2), 180; https://doi.org/10.3390/min15020180 - 15 Feb 2025

Cited by 1 | Viewed by 448

Abstract

This paper presents a new account of the mineralogy of the bat guano deposit in Gaura cu Muscă Cave, Locvei Mountains, Romania. The cave, which, in its main proportion, is a wet, “live” cave, has a dry portion hosting guano. Biogenic leucophosphite is one of the main compounds of the fossil bat guano association in the cave, where it occurs together with hydroxylapatite, taranakite, ardealite, calcite, quartz and illite (the 2M1 polytype). The mineral species from the cave were characterized by optical methods, scanning electron microscopy, wet-chemical analysis, X-ray powder diffraction, Fourier-transform infrared and inductively coupled plasma – atomic emission spectrometry. The crystal-chemical formula of leucophosphite from Gaura cu Muscă is [K_0.978Na_0.003(NH₄)_0.014](Al_0.085Fe_1.903Mg_0.001Mn_0.006)(PO₄)₂(OH)_0.973·2H₂O. The cell parameters calculated for the same sample are a = 9.813(6) Å, b = 9.749(6) Å, c = 9.631(9) Å and β = 102.30(2)°. The infrared spectrum affords the presence of (PO₄)³⁻, (HPO₄)²⁻, (NH₄)⁺ and (OH)⁻ ions, together with H₂O molecules. The band multiplicity on the IR absorption spectrum suggests that the phosphate groups in the structure have C_s punctual symmetry. The host deposit was formed under extremely “dry” conditions that favored a sharp decrease in the pH of solutions derived from the guano mass. Full article

(This article belongs to the Special Issue Microbial Biomineralization and Organimineralization)

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18 pages, 3501 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Enhancing Biogenic Scorodite Formation Using Waste Iron Sludge: A Sustainable Approach for Arsenic Immobilization

by Kazuma Kimura and Naoko Okibe

Minerals 2025, 15(1), 56; https://doi.org/10.3390/min15010056 - 7 Jan 2025

Viewed by 782

Abstract

Arsenic (As) contamination in water poses significant environmental and health risks, particularly in mining regions. Scorodite (FeAsO₄·2H₂O) is a highly stable compound for As immobilization, traditionally synthesized under high As concentrations and extreme conditions, such as elevated temperatures and pressures. This study explores a sustainable alternative by utilizing Fe-sludge, a waste by-product from acid mine drainage (AMD) treatment, as a novel Fe source for biogenic scorodite formation mediated by the thermo-acidophilic archaeon Acidianus brierleyi. Through a systematic evaluation of Fe-sludge incorporation, the study investigates its impact on microbial activity, As immobilization efficiency, and scorodite crystallization mechanisms. Liquid and solid analyses demonstrate that Fe-sludge enhances the reaction rate and crystallinity of scorodite while bypassing the induction period required in Fe²⁺-only systems. Cross-sectional SEM imaging and EXAFS analysis reveal dynamic transformations on the Fe-sludge surface, supporting faster As adsorption and scorodite nucleation through Fe-S intermediates. Despite potential challenges to microbial activity at higher Fe-sludge concentrations, optimized conditions successfully balance cell viability and Fe utilization. This approach offers an eco-friendly, cost-effective pathway for As immobilization by repurposing AMD sludge, contributing to sustainable resource management and reducing environmental impact. Full article

(This article belongs to the Special Issue Microbial Biomineralization and Organimineralization)

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17 pages, 5201 KiB

Open AccessArticle

Simulated Experimental Study on the Removal of Methylene Blue-Cu(II) Composite Pollution by Magnetized Vaterite

by Xiaodan He, Mingyang Hu, Yu Cui, Xingxing Wang and Bin Lian

Minerals 2024, 14(11), 1142; https://doi.org/10.3390/min14111142 - 11 Nov 2024

Viewed by 989

Abstract

The combined pollution of organics and heavy metals represents a significant environ-mental problem that has attracted widespread attention. This explores the treatment of methylene blue (MB) and Cu(II), which are common pollutants in dye wastewater, and the recycling of Cu. A magnetized vaterite (V-M) was synthesized using Bacillus velezensis, and its structure and magnetic performance were investigated. The effects and mechanisms of removing MB-Cu(II) composite pollution using V-M and H₂O₂ in combination were estimated. The results indicated that V-M is a combination of organic and inorganic substances, with 21.5 wt% organic matter and multiple organic functional groups, including O-H, -SH, and others. The combination of V-M and H₂O₂ can achieve a maximum removal percentage of 90% for MB-Cu(II) pollution. The analysis showed that MB was oxidized by the ·OH generated from the H₂O₂-based Fenton-like reaction, and was catalyzed by the Fe₃O₄ in V-M. The immobilization of Cu(II) by V-M was mostly realized through the binding of the organic substances on the surface of the V-M, multilayer adsorption, and a replacement reaction with Ca(II). Magnetic separation and the addition of diluted HCl were used for the recycling of the Cu(II) enriched by V-M, with a recycling percentage reaching 85%. This study introduced a novel approach to the remediation of MB-Cu(II) composite pollution, and the recycling of Cu(II). Full article

(This article belongs to the Special Issue Microbial Biomineralization and Organimineralization)

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19 pages, 7350 KiB

Open AccessArticle

Inhibitory Effects of Polysaccharides on the Dolomitization Reaction of Calcite at 200 °C

by Yang Wei and Hiromi Konishi

Minerals 2024, 14(7), 721; https://doi.org/10.3390/min14070721 - 18 Jul 2024

Viewed by 933

Abstract

This study investigates the impact of dissolved carboxymethyl cellulose (CMC) and agar on the dolomitization reaction of calcite at 200 °C. Previous studies have suggested that CMC and agar promote dolomite precipitation at room temperature. However, this study found that their decomposition products hinder the reaction at 200 °C, with uncertainty about their role at other temperatures. The inhibitory effect of the decomposition products could be attributed to their adsorption onto calcite surfaces, which hinders their dissolution. This results in a longer reaction induction period and replacement period. Regression analysis demonstrates that the 0.1 g/L agar and 0.2 g/L CMC series decrease the cation ordering rate of dolomite produced from synthetic calcite when compared with series without polysaccharides. In contrast, the 0.1 g/L CMC series shows a slight increase in the cation ordering rate compared with series without polysaccharides. The findings of this study suggest a notable potential impact of the decomposition products of polysaccharides on the ordering of dolomite, although it is uncertain whether they inhibit this ordering process. The inhibitory effect observed in the decomposition products of CMC and agar could also exist in the decomposition products of the extracellular polymeric substances (EPS) and bacteria cell walls found in sedimentary rocks during burial diagenesis. Therefore, further research is necessary to understand the role of EPS and bacteria cell walls in dolomitization, since their impact is not always predictable. Full article

(This article belongs to the Special Issue Microbial Biomineralization and Organimineralization)

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22 pages, 10040 KiB

Open AccessArticle

Bacteria-Driven Fossil Ecosystems as Paleoindicators of Active Continental Margins and the Role of Carbonate Sediment-Hosted Vents in Geodynamic Reconstructions

by László Bujtor, Ildikó Gyollai, Máté Szabó, Ivett Kovács and Márta Polgári

Minerals 2024, 14(2), 125; https://doi.org/10.3390/min14020125 - 24 Jan 2024

Cited by 2 | Viewed by 1583

Abstract

Continental rifting of the Tisza microplate started during the Late Jurassic and resulted in phreatic eruptions, peperite, and the construction of a volcanic edifice in the Early Cretaceous in the Mecsek Mountains (South Hungary). In the SE direction from the volcanic edifice at Zengővárkony, a shallow marine (depth 100–200 m) carbonate sediment hosted a vent environment, and iron ore deposition occurred at the end of the Valanginian to early Hauterivian, hosting a diverse, endemic fauna of approximately 60 species. The detailed mineralogical analysis of the transport conduits included Fe oxides (ferrihydrite, goethite, hematite, and magnetite), quartz, mixed carbonate, pyrite, feldspar, Fe-bearing clay minerals, apatite, sulfates (barite, gypsum, and jarosite), and native sulfur. Filamentous, microbially mediated microtextures with inner sequented, necklace-like spheric forms (diameter of 1 μm) and bacterial laminae are also observed inside decapod crustacean coprolites (Palaxius tetraochetarius) and in the rock matrix. This complex ecological and mineralogical analysis provided direct evidence for the presence of bacteria in fossil sediment-hosted vent (SHV) environments on the one hand and for the intimate connection between bacteria and decapod crustaceans in hydrothermal environments 135 Ma before. This observation completes the fossil food chain of chemosynthesis-based ecosystems, from primary producers to the top carnivores reported for the first time from this locality. Full article

(This article belongs to the Special Issue Microbial Biomineralization and Organimineralization)

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17 pages, 14676 KiB

Open AccessArticle

Authigenic Mineral Formation in Aquifers near the Uranium Sludge Storage Facility of Chepetsky Mechanical Plant during the Formation of a Biogeochemical Barrier in a Laboratory and Field Experiment

by Grigory Artemiev and Alexey Safonov

Minerals 2023, 13(10), 1319; https://doi.org/10.3390/min13101319 - 12 Oct 2023

Cited by 3 | Viewed by 1345

Abstract

In this work, authigenic microbial mineral formation in groundwater near the uranium sludge storage at SC Chepetsky Mechanical Plant (ChMP) (Glazov, Russia) was analysed in field and laboratory experiments using thermodynamic modelling when the microbial community was activated by a mixture of acetate, glucose and whey. It was found that the mineral basis of the barrier consisted of aggregated soil particles with freshly deposited phases of carbonate and sulphide minerals of different degrees of crystallinity. An important factor in the formation of calcium phases is microbial denitrification, which is accompanied by an increase in pH values of the medium. The main factors of uranium immobilisation in the biogeochemical barrier were revealed, including its reduction to insoluble forms of uranium dioxide, adsorption on ferrous and sulphide-ferrous minerals, as well as the formation of phosphate phases through the addition of phosphorus-containing whey and co-precipitation or co-crystallisation in calcite phases. Full article

(This article belongs to the Special Issue Microbial Biomineralization and Organimineralization)

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13 pages, 1707 KiB

Open AccessArticle

Saprotrophic Fungus Induces Microscale Mineral Weathering to Source Potassium in a Carbon-Limited Environment

by Jocelyn A. Richardson, Christopher R. Anderton and Arunima Bhattacharjee

Minerals 2023, 13(5), 641; https://doi.org/10.3390/min13050641 - 5 May 2023

Cited by 2 | Viewed by 2852

Abstract

Plants rely on potassium for many critical biological processes, but most soils are potassium limited. Moving potassium from the inaccessible, mineral-bound pool to a more bioavailable form is crucial for sustainably increasing local potassium concentrations for plant growth and health. Here, we use a synthetic soil habitat (mineral doped micromodels) to study and directly visualize how the saprotrophic fungus, Fusarium sp. DS 682, weathers K-rich soil minerals. After 30 days of fungal growth, both montmorillonite and illite (secondary clays) had formed as surface coatings on primary K-feldspar, biotite, and kaolinite grains. The distribution of montmorillonite differed depending on the proximity to a carbon source, where montmorillonite was found to be associated with K-feldspar closer to the carbon (C) source, which the fungus was inoculated on, but associated with biotite at greater distances from the C source. The distribution of secondary clays is likely due to a change in the type of fungal exuded organic acids; from citric to tartaric acid dominated production with increasing distance from the C source. Thus, the main control on the ability of Fusarium sp. DS 682 to weather K-feldspar is proximity to a C source to produce citric acid via the TCA cycle. Full article

(This article belongs to the Special Issue Microbial Biomineralization and Organimineralization)

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13 pages, 5987 KiB

Open AccessArticle

Co-Precipitation of Cd, Cr, Pb, Zn, and Carbonates Using Vibrio harveyi Strain Isolated from Mediterranean Sea Sediment

by Mazhar Ali Jarwar, Pablo Del Buey, M. Esther Sanz-Montero, Stefano Dumontet, Elena Chianese and Vincenzo Pasquale

Minerals 2023, 13(5), 627; https://doi.org/10.3390/min13050627 - 29 Apr 2023

Cited by 9 | Viewed by 2537

Abstract

Heavy metal contamination is listed among the most alarming threats to the environment and human health. The detrimental effects of heavy metals in the natural environment span from a reduction of biodiversity to toxic effects on marine life—through microplastic born heavy metals, to impairment of microbial activity in the soil, and to detrimental effects on animal reproduction. A host of different chemical and biological technologies have been proposed to alleviate environmental contamination by heavy metals. Relatively less attention has been paid to the microbial precipitation of heavy metals, as a side mechanism of the most general process of microbially induced calcite precipitation (MICP). This process is currently receiving a great deal of interest from both a theoretical and practical standpoint, because of its possible practical applications in concrete healing and soil consolidation, and its importance in the more general framework of microbial induced mineral precipitation. In this study, we analyse the ability of the marine bacteria Vibrio harveyi in co-precipitating CaCO₃ minerals, together with Cd, Cr, Pb, and Zn added in form of nitrates, from solutions containing CaCl₂. The precipitated carbonatic minerals were a function of the different heavy metals present in the solution. The process of co-precipitation appears to be rather effective and fast, as the concentrations of the 4 heavy metals were reduced in 2 days by 97.2%, on average, in the solutions. This bioremediation technology could be used as environmental friendly procedure to de-contaminate suitable environmental matrices. The high performance of this process makes it particularly interesting for an upscaling from lab to field. Full article

(This article belongs to the Special Issue Microbial Biomineralization and Organimineralization)

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