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The Microbiology of Biomining: Microbial Communities, Consortia and Species Involved...
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The Microbiology of Biomining: Microbial Communities, Consortia and Species Involved in Mineral Processing

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 March 2024) | Viewed by 14292

Special Issue Editors

Dr. María Sofía Urbieta

E-Mail Website
Guest Editor
CINDEFI (CCT La Plata-CONICET, Facultad de Ciencias Exactas—UNLP), Universidad Nacional de La Plata (UNLP), Buenos Aires B8508, Argentina
Interests: environmental microbiology; extremophilic microorganisms; biomining; bioremediation of heavy metals
Special Issues, Collections and Topics in MDPI journals
Dr. Laura Castro

E-Mail Website
Guest Editor
Department of Chemical and Materials Engineering, Complutense University of Madrid, Av. Complutense s/n, 28040 Madrid, Spain
Interests: bioleaching; biosorption; bioremediationof toxic metals; biosynthesis of metallic nanoparticles
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biomining, traditionally the use of microorganisms for the extraction of metals from sulphide minerals, is undoubtedly a robust, economic, and environmentally friendly alternative to traditional extractive technologies. However, this green biotechnology is facing new challenges as shallow, more accessible deposits are failing and worldwide concern for the accumulation of contaminated wastes, the generation of acid mine drainage that contaminates soils and water bodies even kilometres away and the use of fresh water is increasing, making regulations stricter, to mention only some major issues. This context presents challenges to the scientific community working on biomining at two levels that go hand in hand: one is the need to find and unconventional metal deposits and make them exploitable, and other is associated with the microbial species, being able to work on them, which is the focus of this Special Issue.

Researchers and companies working on biomining are putting forward great effort and resources to find alternative sources for the extraction of metals, including low-grade minerals, abandoned tailing, complex minerals with difficult-to-handle toxic elements such as arsenic, polymetallic mineral deposits in deep surfaces or deep sea that contain rare earth elements or are rich in manganese, or even the alternative of exploring asteroids or planets in outer space. Something similar is happening with the attempt to replace, at least partially, the use of fresh water by sea water in biomining operations. All these changes that traditional biomining is confronting require artificially or naturally adapted microorganisms, not only to tolerate but also to successfully develop under these complex conditions.

Luckily, these challenges are occurring in the era of meta-omics that allows a deep understanding of the structure, interrelation, and metabolic processes of microbial communities and single species at the levels of genetic material, proteins, and other metabolites. On the other hand, bioengineering is finally coming up with strategies to genetically modify acidophiles, expanding the toolbox to make such microbial species more tolerant to the multiple unfavourable conditions found in the metal matrixes that modern bioleaching is experimenting with.

Finally, the exhaustive exploration of extreme environments combined with the application of state-of-the-art technologies from different fields (omics, analytics, cytometry, and microscopy, among others) is allowing us to increase the knowledge of microbial diversity, community structure, and even single rare habitants, which can be used to develop novel alternatives for different biotechnologies, including biomining.

In this Special Issue, we will be dealing with the most recent advances in the characterisation and uses of microbial communities, artificial consortia, and isolated species capable of mineral processing in the described new era of biomining.

Dr. María Sofía Urbieta
Dr. Laura Castro
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
  • omics in biomining
  • mineral-microbe interactions
  • microbial diversity
  • microbial consortia

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Published Papers (6 papers)

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Research

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13 pages, 2060 KiB  
Article
Using Manganese Oxidizing Fungi to Recover Metals from Electronic Waste
by Sarah A. Doydora, Oliver Baars, Marc A. Cubeta and Owen W. Duckworth
Minerals 2024, 14(1), 111; https://doi.org/10.3390/min14010111 - 20 Jan 2024
Cited by 1 | Viewed by 1526
Abstract
Discarded electronic materials (e-waste) contain economically valuable metals that can be hazardous to people and the environment. Current e-waste recycling approaches involve either energy-intensive smelting or bioleaching processes that capture metals in their dissolved forms. Our study aimed to use Mn oxidizing fungi [...] Read more.
Discarded electronic materials (e-waste) contain economically valuable metals that can be hazardous to people and the environment. Current e-waste recycling approaches involve either energy-intensive smelting or bioleaching processes that capture metals in their dissolved forms. Our study aimed to use Mn oxidizing fungi for recovering metals from e-waste that could potentially transform recycled metals directly into solid forms. We hypothesized that Mn oxidizing fungi can extract metals through chelation by siderophores and subsequent metal (or metal-chelate) adsorption to Mn oxides produced by fungi. Pure cultures of the three fungal species examined were grown on solidified Leptothrix medium with or without ground lithium ion batteries and incubated under ambient room temperature. The results showed Mn and Co were recovered at the highest concentrations of 8.45% and 1.75%, respectively, when grown with Paraconiothyrium brasiliensis, whereas the greatest concentration of Cu was extracted by Paraphaeosphaeria sporulosa at 20.6% per weight of e-waste-derived metals. Although metal-siderophore complexes were detected in the fungal growth medium, metal speciation data suggested that these complexes only occurred with Fe. This observation suggests that reactions other than complexation with siderophores likely solubilized e-waste metals. Elemental mapping, particularly of P. brasiliensis structures, showed a close association between Mn and Co, suggesting potential adsorption or (co)precipitation of these two metals near fungal mycelium. These findings provide experimental evidence for the potential use of Mn oxidizing fungi in recycling and transforming e-waste metals into solid biominerals. However, optimizing fungal growth conditions with e-waste is needed to improve the efficiency of metal recovery. Full article
(This article belongs to the Special Issue The Microbiology of Biomining: Microbial Communities, Consortia and Species Involved in Mineral Processing)
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13 pages, 3306 KiB  
Article
Exploring the Development of Astrobiology Scientific Research through Bibliometric Network Analysis: A Focus on Biomining and Bioleaching
by Luca Tonietti, Bernardo Barosa, Emiliano Pioltelli, Donato Giovannelli, Giovanni Covone, Paola Di Donato, Angelina Cordone, Laura Inno, Christian Magliano, Stefano Fiscale, Maria Teresa Muscari Tomajoli, Gaetana Napolitano, Alice Maria Piccirillo, Vincenzo Della Corte, Rosa Santomartino and Alessandra Rotundi
Minerals 2023, 13(6), 797; https://doi.org/10.3390/min13060797 - 11 Jun 2023
Cited by 2 | Viewed by 3226
Abstract
Our understanding of the diversity of life on our planet and the possibility of finding or sustaining life elsewhere in the universe plays a central role in supporting human space settlement and exploration. Astrobiology and its outcomes require a multidisciplinary and comprehensive approach, [...] Read more.
Our understanding of the diversity of life on our planet and the possibility of finding or sustaining life elsewhere in the universe plays a central role in supporting human space settlement and exploration. Astrobiology and its outcomes require a multidisciplinary and comprehensive approach, in which the microbial, geological, chemical, astronomical, and physical domains of research are interlinked. An example of the applications of astrobiology and space microbiology is the use of extremophiles for in situ resource utilization through biomining and bioleaching. To better understand the multidisciplinary research landscape in this area, we quantitatively reviewed the global scientific literature on astrobiology, with a focus on biomining and bioleaching through bibliometric network analysis, investigating patterns and trends in its development over time. The network analysis of keyword co-occurrence highlights different connecting and overlapping clusters, illustrating the multidisciplinary character of astrobiology. Temporal analyses show a recent focus on topics related to microbiology and geomicrobiology, emphasizing the role that these fields will play in future astrobiology research. In conclusion, astrobiology, biomining, and bioleaching research are currently addressing the recognition of these techniques as valuable tools for biotechnological applications, expected to play a crucial role in long-term human space exploration. Full article
(This article belongs to the Special Issue The Microbiology of Biomining: Microbial Communities, Consortia and Species Involved in Mineral Processing)
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17 pages, 2733 KiB  
Article
Native Bacteria Isolated from Phosphate Deposits Reveal Efficient Metal Biosorption and Adhesion to Ore Particles
by Hakim Rabia, Malek Ould Hamou, Katarzyna Kasperkiewicz, Tomasz Krzykawski, Monika Malicka, Izabela Potocka, Iryna Bodnaruk, Amira Merchichi, Magdalena Skowronek and Maria Augustyniak
Minerals 2023, 13(3), 388; https://doi.org/10.3390/min13030388 - 10 Mar 2023
Cited by 3 | Viewed by 1970
Abstract
Mining and processing phosphate ore are among the essential branches of the economy in some developing countries, including Algeria. Conventional ore beneficiation methods can harm the environment by consuming tremendous amounts of water resources (during washing and flotation), potentially hazardous chemicals, and thermal [...] Read more.
Mining and processing phosphate ore are among the essential branches of the economy in some developing countries, including Algeria. Conventional ore beneficiation methods can harm the environment by consuming tremendous amounts of water resources (during washing and flotation), potentially hazardous chemicals, and thermal energy. Mine water contains toxic metals that, when released, interfere with environmental functioning. Therefore, in line with environmental needs, conventional methods should be gradually replaced with safe biotechnological processes. This study aimed to investigate the biosorption and adhesion abilities of native microorganisms isolated from Djebel Onk ore (Algeria). The examined bacterial strains differed in their metal accumulation efficiency. The incubation of phosphate ore with the native strain Bacillus HK4 significantly increased the recovery of Mg and Cd (at pH 7, 8147.00 and 100.89 µg/g−1, respectively). The HK4 strain also revealed better adhesion to the ore particles than the reference strain of Bacillus subtilis. Thus, biosorption could be more effective when using the native HK4 strain, which can remove Cd and/or Mg over a pH 4–10 range. Moreover, concerning the unique adhesion capacity of HK4, the strain can be considered in the design of bioflotation methods, as well as in the development of an eco-friendly method of ore and post-flotation waste beneficiation. Full article
(This article belongs to the Special Issue The Microbiology of Biomining: Microbial Communities, Consortia and Species Involved in Mineral Processing)
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12 pages, 627 KiB  
Article
New Features of Acidophilic Bacteria of the Genus Sulfobacillus: Polysaccharide Biosynthesis and Degradation Pathways
by Anna Panyushkina and Maxim Muravyov
Minerals 2023, 13(2), 255; https://doi.org/10.3390/min13020255 - 11 Feb 2023
Cited by 3 | Viewed by 1857
Abstract
Bacteria of the genus Sulfobacillus are predominant members of acidophilic microbial communities involved in the bioprocessing of sulfide raw materials. Genomic analysis of different Sulfobacillus species revealed a starch/glycogen GlgE-dependent biosynthesis pathway of α-glucans from trehalose in S. thermotolerans and S. thermosulfidooxidans. [...] Read more.
Bacteria of the genus Sulfobacillus are predominant members of acidophilic microbial communities involved in the bioprocessing of sulfide raw materials. Genomic analysis of different Sulfobacillus species revealed a starch/glycogen GlgE-dependent biosynthesis pathway of α-glucans from trehalose in S. thermotolerans and S. thermosulfidooxidans. The key enzyme of this pathway, a fused maltose-trehalose/α-amylase protein, was not encoded in the genomes of other Sulfobacillus bacteria. At the same time, the presence of all genes encoding enzymes for α-glucan decomposition allowed the prediction of polysaccharide degradation pathways in these two species. Despite the optimum mixotrophic type of metabolism, a gradual adaptation of Sulfobacillus bacteria to polysaccharides resulted in their active organotrophic growth. Moreover, the enzyme assay determined the activities of the extracellular enzymes involved in glycogen and starch degradation. In acidophilic communities of natural and industrial habitats, an essential function of polysaccharides in the composition of extracellular polymeric substances of slime matrices is to promote the attachment of the microbial cells to solid surfaces, such as mineral particles. Polysaccharides can also be storage compounds used for energy and carbon metabolism under specific environmental conditions. Understanding the metabolic capabilities of Sulfobacillus bacteria in consuming and synthesizing α-glucans, which are provided in this study, is of fundamental importance in understanding acidophilic microbial communities and their application in practice. Full article
(This article belongs to the Special Issue The Microbiology of Biomining: Microbial Communities, Consortia and Species Involved in Mineral Processing)
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15 pages, 2131 KiB  
Article
Bioleaching of Sulfide Minerals by Leptospirillum ferriphilum CC from Polymetallic Mine (Armenia)
by Arevik Vardanyan, Anna Khachatryan, Laura Castro, Sabine Willscher, Stoyan Gaydardzhiev, Ruiyong Zhang and Narine Vardanyan
Minerals 2023, 13(2), 243; https://doi.org/10.3390/min13020243 - 8 Feb 2023
Cited by 4 | Viewed by 2678
Abstract
A strain of Leptospirillum sp. CC previously isolated from Akhtala polymetallic ore (Armenia) was studied. The main morphological and physiological characteristics of CC were revealed. The optimal growth temperature was 40 °C and optimal pH 1.5. A phylogenetic analysis based on 16S rRNA [...] Read more.
A strain of Leptospirillum sp. CC previously isolated from Akhtala polymetallic ore (Armenia) was studied. The main morphological and physiological characteristics of CC were revealed. The optimal growth temperature was 40 °C and optimal pH 1.5. A phylogenetic analysis based on 16S rRNA gene sequences (GenBank ID OM272948) showed that isolate CC was clustered with L. ferriphilum and possessed 99.8% sequence similarity with the strain L. ferriphilum OL12-2 (KF356024). The molar fraction of DNA (G + C) of the isolate was 58.5%. Bioleaching experiment indicates that L. ferriphilum CC can oxidize Fe(II) efficiently, and after 17 days, 44.1% of copper and 91.4% of iron are extracted from chalcopyrite and pyrite, respectively. The efficiency of L. ferriphilum CC in pyrite oxidation increases 1.7 times when co-cultivated with At. ferrooxidans ZnC. However, the highest activity in pyrite oxidation shows the association of L.ferriphilum CC with heterotrophic Acidocella sp. RBA bacteria. It was shown that bioleaching of copper and iron from chalcopyrite by association of L. ferriphilum CC, At. ferrooxidans ZnC, and At. albertensis SO-2 in comparison with pure culture L. ferriphilum CC for 21 days increased about 1.2 and 1.4–1.6 times, respectively. Full article
(This article belongs to the Special Issue The Microbiology of Biomining: Microbial Communities, Consortia and Species Involved in Mineral Processing)
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Review

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25 pages, 2591 KiB  
Review
The Role of Biomodification in Mineral Processing
by Agnieszka Pawlowska and Zygmunt Sadowski
Minerals 2023, 13(10), 1246; https://doi.org/10.3390/min13101246 - 23 Sep 2023
Cited by 1 | Viewed by 1938
Abstract
Increasing environmental concern forces the reduction in the share of synthetic surfactants in the production of various industries, including mineral processing, by replacing them with more environmentally friendly compounds of biological origin. Several studies on the use of biosurfactants in mineral processing are [...] Read more.
Increasing environmental concern forces the reduction in the share of synthetic surfactants in the production of various industries, including mineral processing, by replacing them with more environmentally friendly compounds of biological origin. Several studies on the use of biosurfactants in mineral processing are currently available in the literature, but they contain limited information related to the physicochemistry of these processes. Therefore, this review aims to summarise publications from the last decade related to the role of microorganisms and their metabolic products in mineral surface modification applied in mineral processing. Theoretical principles of bacteria–mineral interactions are presented. Salt-type, sulphide, and oxide minerals were discussed with greater attention to the physicochemistry of biosurfactant–mineral interactions, such as the wettability and surface charge. The advantages and disadvantages of using bacterial cells and surface-active microbial compounds were proposed. The trends and challenges of biomodification in flotation and flocculation were discussed. Full article
(This article belongs to the Special Issue The Microbiology of Biomining: Microbial Communities, Consortia and Species Involved in Mineral Processing)
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