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Minerals
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Bio-Transformation and Mineralization Induced by Microorganisms
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Bio-Transformation and Mineralization Induced by Microorganisms

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

Deadline for manuscript submissions: closed (15 October 2019) | Viewed by 26722

Special Issue Editor

Prof. Dr. Yul Roh

E-Mail Website
Guest Editor
Department of Earth and Environmental Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
Interests: biomineralization (biologically induced mineralization and biologically controlled mineralization); reduction and precipitation of redox-sensitive metals and radionuclides; metal recover; mineral microorganisms
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microorganisms can obtain energy to support growth from the dissimilatory reduction of Mn(IV), Fe(III), and any number of multivalent trace metals and the radionuclides. Understanding the mechanisms of bio-transformation of the various chemical forms of toxic metals and radionuclides present in wastes and contaminated soils and water has led to the development of novel bioremediation processes. Microorganisms form immense varieties of authigenic minerals such as oxides, clays, carbonates, phosphates, sulfates, and sulfides. Modern elemental cycles such as Fe, Mn, Si, Ca, P, C and S are all affected by bio-mineralization processes.

We invite contributions on, but not limited to, biogeochemical and mineralogical studies of the biotransformation of Mn(IV), Fe(III), redox-sensitive metals and radionuclides at both the laboratory and field scales. We especially encourage papers on the development of novel characterization methods of the bio-transformation of redox-sensitive metals/radionuclides and bio-minerals and/or novel applications of microbe–metal/radionuclide interactions and biomineralization with an interdisciplinary perspective.

Prof. Dr. Yul Roh
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

  • Bio-transformation
  • Bio-mineralization
  • Microorganisms
  • Heavy metals
  • Radionuclides
  • Bioremediation
  • Metal recovery

Published Papers (8 papers)

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Research

26 pages, 6606 KiB  
Article
Bio-Precipitation of Carbonate and Phosphate Minerals Induced by the Bacterium Citrobacter freundii ZW123 in an Anaerobic Environment
by Bin Sun, Hui Zhao, Yanhong Zhao, Maurice E. Tucker, Zuozhen Han and Huaxiao Yan
Minerals 2020, 10(1), 65; https://doi.org/10.3390/min10010065 - 13 Jan 2020
Cited by 15 | Viewed by 3439
Abstract
In this study, a facultative anaerobic strain isolated from marine sediments and identified as Citrobacter freundii, was used to induce the precipitation of carbonate and phosphate minerals in the laboratory under anaerobic conditions. This is the first time that the ability of C. [...] Read more.
In this study, a facultative anaerobic strain isolated from marine sediments and identified as Citrobacter freundii, was used to induce the precipitation of carbonate and phosphate minerals in the laboratory under anaerobic conditions. This is the first time that the ability of C. freundii ZW123 to precipitate carbonate and phosphate minerals has been demonstrated. During the experiments, carbonic anhydrase, alkaline phosphatase and ammonium released by the bacteria not only promoted an increase in pH, but also drove the supersaturation and precipitation of carbonate and phosphate minerals. The predominant bio-mediated minerals precipitated at various Mg/Ca molar ratios were calcite, vaterite, Mg-rich calcite, monohydrocalcite and struvite. A preferred orientation towards struvite was observed. Scanning transmission electron microscopy (STEM) and elemental mapping showed the distribution of magnesium and calcium elements within Mg-rich calcite. Many organic functional groups, including C=O, C–O–C and C–O, were detected within the biominerals, and these functional groups were also identified in the associated extracellular polymeric substances (EPS). Fifteen kinds of amino acid were detected in the biotic minerals, almost identical to those of the EPS, indicating a close relationship between EPS and biominerals. Most amino acids are negatively charged and able to adsorb cations, providing an oversaturated microenvironment to facilitate mineral nucleation. The X-ray photoelectron spectroscopy (XPS) spectrum of struvite shows the presence of organic functional groups on the mineral surface, suggesting a role of the microorganism in struvite precipitation. The ZW123 bacteria provided carbon and nitrogen for the formation of the biotic minerals through their metabolism, which further emphasizes the close relationship between biominerals and the microorganisms. Thermal studies showed the enhanced thermal stability of biotic minerals, perhaps due to the participation of the bacteria ZW123. The presence of amino acids such as Asp and Glu may explain the high magnesium content of some calcites. Molecular dynamics simulations demonstrated that the morphological change and preferred orientation were likely caused by selective adsorption of EPS onto the various struvite crystal surfaces. Thus, this study shows the significant role played by C. freundii ZW123 in the bioprecipitation of carbonate and phosphate minerals and provides some insights into the processes involved. Full article
(This article belongs to the Special Issue Bio-Transformation and Mineralization Induced by Microorganisms)
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20 pages, 1596 KiB  
Article
Use of a Zeolite and Molecular Sieve to Restore Homeostasis of Soil Contaminated with Cobalt
by Edyta Boros-Lajszner, Jadwiga Wyszkowska and Jan Kucharski
Minerals 2020, 10(1), 53; https://doi.org/10.3390/min10010053 - 06 Jan 2020
Cited by 8 | Viewed by 2315
Abstract
Since contamination of soil with cobalt disturbs the soil’s biological balance, various types of compounds are being sought that could be used to restore the homeostasis of contaminated soil. The aim of the study was to determine the use of a Bio.Zeo.S.01 zeolite [...] Read more.
Since contamination of soil with cobalt disturbs the soil’s biological balance, various types of compounds are being sought that could be used to restore the homeostasis of contaminated soil. The aim of the study was to determine the use of a Bio.Zeo.S.01 zeolite and molecular sieve in restoring the microbiological and biochemical balance of soil contaminated with cobalt. Soil samples were contaminated with cobalt (CoCl2·6H2O) at 0, 20, 80 mg·kg−1, and a Bio.Zeo.S.01 zeolite and molecular sieve were introduced at 0 and 15 g·kg−1. The soils on which the experiment was conducted were loamy sand and sandy clay loam. The experiment was carried out in two series on soil with and without a crop sown in it. The multiplication of microorganisms and the soil enzymes’ activity were determined on days 25 and 50 (harvest) of the experiment, and the yield of the underground and above-ground parts of maize and chemical and physical properties of soil were determined on the day of harvest. It was found that the microorganisms’ multiplication, enzyme activity, and maize yield were significantly disturbed by the excess of cobalt in the soil regardless of the soil type. The zeolite Bio.Zeo.S.01 used in the study had a smaller impact on microorganisms and soil enzyme activity than the molecular sieve. Cobalt accumulated more in the roots than in the above-ground parts of maize. An addition of sorbents decreased the accumulation of cobalt in maize grown only on sandy clay loam. Full article
(This article belongs to the Special Issue Bio-Transformation and Mineralization Induced by Microorganisms)
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10 pages, 6043 KiB  
Article
Microbially Induced Carbonate Precipitation Using Microorganisms Enriched from Calcareous Materials in Marine Environments and Their Metabolites
by Yumi Kim and Yul Roh
Minerals 2019, 9(12), 722; https://doi.org/10.3390/min9120722 - 21 Nov 2019
Cited by 10 | Viewed by 2585
Abstract
Microbially induced Ca-carbonate precipitation (MICP) in general, refers to a process in which the urease secreted by microbes hydrolyzes urea to ammonium and carbon dioxide. The main objectives of this study were to identify the environmental factors (e.g., microbial growth, cell/metabolite presences, and [...] Read more.
Microbially induced Ca-carbonate precipitation (MICP) in general, refers to a process in which the urease secreted by microbes hydrolyzes urea to ammonium and carbon dioxide. The main objectives of this study were to identify the environmental factors (e.g., microbial growth, cell/metabolite presences, and calcium sources) that control Ca-carbonate formation and to investigate the mineralogical characteristics of the Ca-carbonate precipitated using ureolytic microorganisms cultured in marine environments. The two types of carbonate-forming microorganisms (CFMs), mixed cultures hydrolyzing urea, were enriched from calcareous materials in marine environments. The experiments using a CFM, Sporosarcina pasteurii, was also used for comparison. All the microbes were cultured aerobically in D-1 growth media that included urea. To investigate the effect of microbial growth states on Ca-carbonate precipitation, Ca-acetate was injected into the media before (i.e., lag phase) and after (i.e., stationary phase) microbial growth, and into the soluble microbial products (SMP) solution, respectively. XRD, FT-IR, and SEM-EDS analyses were used for mineralogical characterization of the precipitated Ca-carbonates. Results indicated that the Ca-carbonates, vaterite and/or calcite, precipitated under all the experimental conditions. The fastest precipitation of Ca-carbonates occurred in the SMP solution and formed calcite (size = 5–15 μm). When the concentrations of added Ca-acetate were varied from 0 to 0.5 M, the highest amounts of calcite, 22.8 g/L, were produced when 0.3 M Ca-acetate was injected. Therefore, the environmental factors (e.g., microbial growth, cell/metabolite presences, and calcium sources) could have an effect the rate of formation of Ca-carbonate and the types of carbonate minerals formed. Moreover, the use of cell-free SMP solution is expected to be applicable to Ca-carbonate precipitation in an environment where microbial growth is unfavorable. Full article
(This article belongs to the Special Issue Bio-Transformation and Mineralization Induced by Microorganisms)
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29 pages, 7836 KiB  
Article
Electron Donor Utilization and Secondary Mineral Formation during the Bioreduction of Lepidocrocite by Shewanella putrefaciens CN32
by Edward J. O’Loughlin, Christopher A. Gorski, Theodore M. Flynn and Michelle M. Scherer
Minerals 2019, 9(7), 434; https://doi.org/10.3390/min9070434 - 14 Jul 2019
Cited by 20 | Viewed by 4508
Abstract
The bioreduction of Fe(III) oxides by dissimilatory iron reducing bacteria (DIRB) may result in the production of a suite of Fe(II)-bearing secondary minerals, including magnetite, siderite, vivianite, green rusts, and chukanovite; the formation of specific phases controlled by the interaction of various physiological [...] Read more.
The bioreduction of Fe(III) oxides by dissimilatory iron reducing bacteria (DIRB) may result in the production of a suite of Fe(II)-bearing secondary minerals, including magnetite, siderite, vivianite, green rusts, and chukanovite; the formation of specific phases controlled by the interaction of various physiological and geochemical factors. In an effort to better understand the effects of individual electron donors on the formation of specific Fe(II)-bearing secondary minerals, we examined the effects of a series of potential electron donors on the bioreduction of lepidocrocite (γ-FeOOH) by Shewanella putrefaciens CN32. Biomineralization products were identified by X-ray diffraction, Mössbauer spectroscopy, and scanning electron microscopy. Acetate, citrate, ethanol, glucose, glutamate, glycerol, malate, and succinate were not effectively utilized for the bioreduction of lepidocrocite by S. putrefaciens CN32; however, substantial Fe(II) production was observed when formate, lactate, H2, pyruvate, serine, or N acetylglucosamine (NAG) was provided as an electron donor. Carbonate or sulfate green rust was the dominant Fe(II)-bearing secondary mineral when formate, H2, lactate, or NAG was provided, however, siderite formed with pyruvate or serine. Geochemical modeling indicated that pH and carbonate concentration are the key factors determining the prevalence of carbonate green rust verses siderite. Full article
(This article belongs to the Special Issue Bio-Transformation and Mineralization Induced by Microorganisms)
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10 pages, 1832 KiB  
Article
Selective Mineralization and Recovery of Au(III) from Multi-Ionic Aqueous Systems by Bacillus licheniformis FZUL-63
by Yangjian Cheng, Zhibin Ke, Xiaojing Bian, Jianhua Zhang, Zhen Huang, Yuancai Lv and Minghua Liu
Minerals 2019, 9(7), 392; https://doi.org/10.3390/min9070392 - 28 Jun 2019
Cited by 2 | Viewed by 2346
Abstract
The recovery of precious metals is a project with both economic and environmental significance. In this paper, how to use bacterial mineralization to selectively recover gold from multi-ionic aqueous systems is presented. The Bacillus licheniformis FZUL-63, isolated from a landscape lake in Fuzhou [...] Read more.
The recovery of precious metals is a project with both economic and environmental significance. In this paper, how to use bacterial mineralization to selectively recover gold from multi-ionic aqueous systems is presented. The Bacillus licheniformis FZUL-63, isolated from a landscape lake in Fuzhou University, was shown to selectively mineralize and precipitate gold from coexisting ions in aqueous solution. The removal of Au(III) almost happened in the first hour. Scanning electron microscope with X-ray energy dispersive spectroscopy (SEM/EDS-mapping) results and fourier transform infrared spectroscopy (FTIR) data show that the amino, carboxyl, and phosphate groups on the surface of the bacteria are related to the adsorption of gold ions. X-ray photoelectron spectroscopy (XPS) results implied that Au(III) ions were reduced to those that were monovalent, and the Au(I) was then adsorbed on the bacterial surface at the beginning stage (in the first hour). X-ray diffraction (XRD) results showed that the gold biomineralization began about 10 h after the interaction between Au(III) ions and bacteria. Au(III) mineralization has rarely been influenced by other co-existing metal ions. Transmission electron microscope (TEM) analysis shows that the gold nanoparticles have a polyhedral structure with a particle size of ~20 nm. The Bacillus licheniformis FZUL-63 could selectively mineralize and recover 478 mg/g (dry biomass) gold from aqua regia-based metal wastewater through four cycles. This could be of great potential in practical applications. Full article
(This article belongs to the Special Issue Bio-Transformation and Mineralization Induced by Microorganisms)
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15 pages, 1475 KiB  
Article
Simultaneous Biological and Chemical Removal of Sulfate and Fe(II)EDTA-NO in Anaerobic Conditions and Regulation of Sulfate Reduction Products
by Yu Zhang, Lijian Sun and Jiti Zhou
Minerals 2019, 9(6), 330; https://doi.org/10.3390/min9060330 - 28 May 2019
Cited by 11 | Viewed by 3199
Abstract
In the simultaneous flue gas desulfurization and denitrification by biological combined with chelating absorption technology, SO2 and NO are converted into sulfate and Fe(II)EDTA-NO which need to be reduced in biological reactor. Increasing the removal loads of sulfate and Fe(II)EDTA-NO and converting [...] Read more.
In the simultaneous flue gas desulfurization and denitrification by biological combined with chelating absorption technology, SO2 and NO are converted into sulfate and Fe(II)EDTA-NO which need to be reduced in biological reactor. Increasing the removal loads of sulfate and Fe(II)EDTA-NO and converting sulfate to elemental sulfur will benefit the application of this process. A moving-bed biofilm reactor was adopted for sulfate and Fe(II)EDTA-NO biological reduction. The removal efficiencies of the sulfate and Fe(II)EDTA-NO were 96% and 92% with the influent loads of 2.88 kg SO42−·m−3·d−1 and 0.48 kg NO·m−3·d−1. The sulfide produced by sulfate reduction could be reduced by increasing the concentrations of Fe(II)EDTA-NO and Fe(III)EDTA. The main reduction products of sulfate and Fe(II)EDTA-NO were elemental sulfur and N2. It was found that the dominant strain of sulfate reducing bacteria in the system was Desulfomicrobium. Pseudomonas, Sulfurovum and Arcobacter were involved in the reduction of Fe(II)EDTA-NO. Full article
(This article belongs to the Special Issue Bio-Transformation and Mineralization Induced by Microorganisms)
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11 pages, 2317 KiB  
Article
Environmental Application of Biogenic Magnetite Nanoparticles to Remediate Chromium(III/VI)-Contaminated Water
by Yumi Kim and Yul Roh
Minerals 2019, 9(5), 260; https://doi.org/10.3390/min9050260 - 29 Apr 2019
Cited by 13 | Viewed by 3375
Abstract
The physicochemical characteristics of biogenic minerals, such as high specific surface areas and high reactivity and the presence of a bacterial carrier matrix, make them promising for various applications. For instance, catalysts, adsorbents, oxidants, and reductants. The objective of this study is to [...] Read more.
The physicochemical characteristics of biogenic minerals, such as high specific surface areas and high reactivity and the presence of a bacterial carrier matrix, make them promising for various applications. For instance, catalysts, adsorbents, oxidants, and reductants. The objective of this study is to examine the efficiency of biogenic magnetite nanoparticles (BMNs) that are produced by metal-reducing bacteria for removing chromium. Interactions between ionic chromium (Cr III/VI) and BMNs were examined under different pH values (ranging from pH 2 to pH 12) by using different doses of BMN (0–6 g/L). Chemically synthesized magnetite nanoparticles (CMNs) were used in the experiments for the purpose of comparing them to the BMNs. The results showed that the BMNs had higher Cr(VI) removal efficiency (100%) than the CMNs (82%) after a two-week reaction time. A lower pH and longer reaction time in the Cr-contaminated solution led to a higher Cr(VI) removal efficiency. The Cr(VI) removal efficiency by the BMNs in the Cr-contaminated groundwater was about 94% after a reaction time of two weeks. The BMNs that were coated with organic matter were more effective than the CMNs in leading to adsorption of Cr(III) with electrostatic interactions (82% versus 13%) and in preventing Fe(II) oxidation within the magnetite structure. These results indicate that the BMNs could be used to decontaminate ionic Cr in environmental remediation technologies. Full article
(This article belongs to the Special Issue Bio-Transformation and Mineralization Induced by Microorganisms)
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17 pages, 3230 KiB  
Article
Mycoextraction: Rapid Cadmium Removal by Macrofungi-Based Technology from Alkaline Soil
by Miaomiao Chen, Likun Wang, Junliang Hou, Shushen Yang, Xin Zheng, Liang Chen and Xiaofang Li
Minerals 2018, 8(12), 589; https://doi.org/10.3390/min8120589 - 12 Dec 2018
Cited by 5 | Viewed by 4311
Abstract
Fungi are promising materials for soil metal bioextraction and thus biomining. Here, a macrofungi-based system was designed for rapid cadmium (Cd) removal from alkaline soil. The system realized directed and rapid fruiting body development for subsequent biomass harvest. The Cd removal efficiency of [...] Read more.
Fungi are promising materials for soil metal bioextraction and thus biomining. Here, a macrofungi-based system was designed for rapid cadmium (Cd) removal from alkaline soil. The system realized directed and rapid fruiting body development for subsequent biomass harvest. The Cd removal efficiency of the system was tested through a pot culture experiment. It was found that aging of the added Cd occurred rapidly in the alkaline soil upon application. During mushroom growth, the soil solution remained considerably alkaline, though a significant reduction in soil pH was observed in both Cd treatments. Cd and dissolved organic carbon (DOC) in soil solution generally increased over time and a significant correlation between them was detected in both Cd treatments, suggesting that the mushroom‒substratum system has an outstanding ability to mobilize Cd in an alkaline environment. Meanwhile, the growth of the mushrooms was not affected relative to the control. The estimated Cd removal efficiency of the system was up to 12.3% yearly thanks to the rapid growth of the mushroom and Cd enrichment in the removable substratum. Transcriptomic analysis showed that gene expression of the fruiting body presented considerable differences between the Cd treatments and control. Annotation of the differentially expressed genes (DEGs) indicated that cell wall sorption, intracellular binding, and vacuole storage may account for the cellular Cd accumulation. In conclusion, the macrofungi-based technology designed in this study has the potential to become a standalone biotechnology with practical value in soil heavy metal removal, and continuous optimization may make the system useful for biomining. Full article
(This article belongs to the Special Issue Bio-Transformation and Mineralization Induced by Microorganisms)
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