Biotechnology of Metals: Principles, Recovery Methods and Environmental Concerns

By K.A. Natarajan

Biotechnology of Metals: Principles, Recovery Methods and Environmental Concerns deals with all aspects of metal biotechnology in different areas, such as biogenesis, biomaterials, biomimetic strategies, biohydrometallurgy, mineral biobeneficiation, electrobioleaching, microbial corrosion, human implants, concrete biocorrosion, microbiology of environment pollution, and bioremediation. As the technology of this interdisciplinary science has diversified over the last five years, this book provides a valuable source for scientists and students in a number of disciplines, including geology, chemistry, metallurgy, microbiology, chemical engineering, environment, civil engineering, and biomedical engineering.

• Offers comprehensive coverage of an interdisciplinary subject
• Outlines the role of microbiology and biotechnology in mining, metallurgy, waste disposal and environmental control
• Covers new topics, such as biogenesis, biomaterials processing, the role of micro-organisms in causing corrosion, and much more
• Presents scientifically illustrated experimental research methods in metals biotechnology

• Language: English
• Publisher: Elsevier Science
• Release date: Jun 13, 2018
• ISBN: 9780128040997

K.A. Natarajan

Dr. K.A. Natarajan is presently NASI Senior Scientist- Platinum Jubilee Fellow and Emeritus Professor at the Department of Materials Engineering, Indian Institute of Science, Bangalore, India. He did his M.S. and Ph.D degrees specializing in Mineral beneficiation and Hydrometallurgy from the University of Minnesota, USA. The Indian Institute of Science, Bangalore conferred on him the degree of Doctor of Science in 1992 for his pioneering research contributions in Minerals bioprocessing. He is a Fellow of several academies such as the Indian Academy of Sciences, Indian National Academy of Engineering, and the National Academy of Sciences. He has received several medals and awards such as the National Metallurgist Award by the Ministry of Mines, Govt. of India, National Mineral award by the Ministry of Mines. Govt. of India, Alumni Award of Excellence in Engineering Research by the Indian Institute of Science, Bangalore, Kamani Gold medal of the Indian Institute of Metals and the Hindustan Zinc Gold Medal. He has also been honored with the presentation of Biotech Product and Process Development & Commercialization Award 2003, Dept. of Biotechnology, Govt. of India. He is on the Editorial board of several international journals in the area of mineral processing. His areas of research include mineral processing, hydrometallurgy, minerals bioprocessing, corrosion engineering and environmental control. He has published over 300 research papers in leading international journals in the above areas. He was the Chairman of the Department of Metallurgy, Indian Institute of Science, Bangalore from 1999 to 2004.

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Preface

K.A. Natarajan

This book titled Biotechnology of Metals addresses to the guiding principles, recovery methods, and environmental concerns pertaining to biogenesis of minerals and metals, biomineralization, metals extraction, mineral beneficiation, as well as environmental degradation and protection.

The symbiotic relationship between microbiology and metals is illustrated through an interdisciplinary approach interlinking occurrence of mineral deposits through microbial activity with role of microorganisms in metal extraction, mineral beneficiation, metal corrosion, and environmental pollution and protection. This book contains 14 chapters devoted to biotechnology–materials interface, microbiological aspects of leaching microorganisms, bioleaching mechanisms, methods in biohydrometallurgy, bioleaching technologies for copper, uranium, zinc, nickel, cobalt, and gold, electrochemical concepts in biohydrometallurgy, microbially induced mineral beneficiation, newer and novel applications such as reduction bioleaching, bioprocessing of rare earth elements, industrial wastes as well as polymetallic ores, nodules, and black schists, biofouling and microbially influenced corrosion, and microbial aspects of acid mine drainage and environmental control. A final chapter on experimental and research methods in Metals Biotechnology is added to help students and young researchers in the field. This text book covering the status and developments in the above-mentioned themes has been conceived and prepared to benefit a wider spectrum of readership encompassing students, researchers, teachers, and engineers specializing in mining, metallurgy, materials processing, environmental science, corrosion engineering, and minerals processing.

The author of this book had early developed an international web course titled METALS BIOTECHNOLOGY under National Program of Technology Enhanced Learning (NPTEL) sponsored by the Ministry of Human Resources Development, Government of India through participation of IITs and IISc. The above web lectures have been thoroughly revised, expanded, and updated for the preparation of this text book.

I would like to express my sincere thanks and gratitude to several good friends, colleagues, and students who helped with the design and preparation of this book. Many contributed to the contents of this book in the forms of valuable criticisms, comments, corrections, providing photographs and figures, as well as extending the necessary official permission for reproduction of figures and tables.

Special thanks are due to Petrus J. van Staden, Senior Technical Specialist, HYDROMETALLURGY DIVISION of Mintek for kind help with providing photographs, information on Mintek operations as well as valuable inputs on biohydrometallurgy. Sincere thanks are due to Mr. Jan Van Niekerk, Senior Manager (BIOX), Outotec(Finland)Oy for providing valuable photographs of several bioreactors along with pertinent literature. I thank Mr. Rail Fatkullin and Mr. Wallies Olivier of Biomin South Africa (Pty) Ltd for their valuable advice and help. Permissions to reproduce figures from published literature were provided by Taylor and Francis and many other publishers.

The author would wish to thank Dr. Kostas Marinakis, Ms. Christine McElvenny, Ms. Carly Demetre, and all in the Editorial team of Elsevier for their help, interest, and advice in bringing this book to fruition. Thanks are due to Ms. Deepa Tejaswini for patiently typing all the chapters and revising all figures and tables through computer graphics.

Chapter 1

Introduction—Status and Scope of Metals Biotechnology

Abstract

Status, scope, and relevance of metals biotechnology are outlined in this chapter. Major applications of this interdisciplinary technology include biomining concepts, mineral beneficiation, metals extraction, and understanding and control of environmental degradation and pollution.

Keywords

Metals biotechnology; status; scope

The synergy among the four Ms, Mining, Minerals, Metals, Microorganisms, is what Metals Biotechnology is all about. Biotechnology applied to mineral exploration, metal extraction, and waste disposal finds applications in a number of interrelated areas such as genesis of minerals, bioindicators, and biosensors for mineral deposits, mineral beneficiation, extraction of metals, biofouling, and microbially influenced corrosion as well as environmental degradation and bioremediation of contaminated sites. The subject matter of this text book encompasses the above aspects in a single compendium. It is expected that this text book will be very useful to students, teachers, researchers, and professionals interested in different areas of biotechnology of metals.

Metals biotechnology could provide several innovative alternatives for environmentally benign mining, metal extraction, and materials processing. Many mine- and mineral-inhabiting microorganisms contribute to natural formation and conversion of mineral forms (biogenesis and biomineralization). Microbes have been interacting with metals and minerals for billions of years, participating in the formation of many biomaterials. Microbes have now been recognized as important geological agents, playing significant roles in mineral formation, degradation, sedimentation, geochemical cycling, and weathering. These organisms are capable of mineral dissolution to release metals ions from which pure metals can be obtained (biohydrometallurgy). They are also capable of bringing about selective dissolution of minerals or separation of undesirable mineral constituents from a multimetal-ore matrix (mineral biobeneficiation). When grown in presence of or exposed to minerals, these organisms develop toxic-metal and toxic-mineral tolerance and secrete metal- and mineral-specific bioreagents. Mineral and metal-binding biomolecules find applications in selective mineral and metal separation. Microbial communities near and on the minerals in an ore deposit are a very rich source of genetic information which could be utilized to create synthetic and modified microbiomes that extract, concentrate, and beneficiate metal forms [1–6].

There exist microbe-metal-mineral cycles for metals and elements such as carbon, sulfur, nitrogen, phosphorous, iron, and many others. Metal biotechnological processes have the potential to transform currently uneconomical ore reserves into viable resources. Microorganisms facilitate valuable metal recovery from metal-containing wastes such as slags, tailings, mined overburden, E-wastes, and acid mine drainage.

Rare metal recovery using metal biotechnology has gained prominence recently. Some recent developments in metals biotechnology include urban mining which is a potential method to leach out and recycle precious and base metals from electronic wastes. Bioleaching under low redox potentials and anaerobic conditions as in reductive dissolution has been taken advantage of in recent years [1–6].

Ever-increasing stringent environmental regulations are expected to put pressure for development of metal recycling and recovery processes from waste streams and urban and industrial wastes. Metals biotechnology will definitely fit in this scheme of things. Key advantages of microbial processes for metal recovery include specificity, energetic, cost effectiveness, and environmental acceptability. However, challenges associated with complex wastes and toxicity problems need to be addressed to.

Innovations in metals biotechnology could provide innovative alternatives to changing scenarios in metals production from exploited difficult mines and wastes. Enhanced exploration costs coupled with location of economic ore deposits at greater depths have created problems in recent years. Average grades of major mineral deposits have been decreasing. Mining ocean floors and terrestrial deeper depths have imposed practical constraints. Other than scarce primary mineral deposits, amounts of metal containing wastes generated by mining and metallurgical industries have indeed become staggering. Besides, mined overburden containing lean grade rocky mass accumulated due to years of mining need to be tackled as a source of strategic metals and environmental threat. Mining from sea water, ocean floors, recycling of used metal components and wastes as well as recovery from wastes tailings, slags, and effluents may became critical issues in the near feature. Recovery of scarce elements (precious and rare-earth metals) from electronic wastes and also from process streams has already become a recent trend of great significance.

Biomining and bioremediation have become familiar terms in metals biotechnology to describe microbially mediated metal extraction and decontamination of polluted sites. Novel biotechnological processes developed over the past two decades have the potential to redefine the metal extraction sequences currently being followed.

Major mechanisms through which mining microbes interact with minerals and metals still remain complex, whether related to bioleaching, biofouling, or microbially influenced corrosion. Besides, it has now been well established that microbes have been interacting with metals and minerals for billions of years under the earth’s crust and ocean sediments, playing a major role in the evolution of minerals. There are several examples for biomineral formation and biogenesis. From the biology-metals-materials interface, we have just begun to learn the art of mineral beneficiation, metal extraction, materials processing, and environmental consequences. Even though only a few metals such as copper, uranium, gold, cobalt, nickel, and zinc are now commercially extracted from sulfide mineral containing ores and concentrates using metals biotechnology, their application has been expanding rapidly in recent years to treat complex multimetal containing deposits, process streams and processed wastes. Application of biohydrometallurgy to nonsulfide ores is also gaining attention.

Keeping in mind the enormous scope of metal biotechnology as outlined earlier, the following aspects are discussed in this book with emphasis on industrial applications and environmental relevance.

• Biotechnology-materials interface illustrating role of microorganisms in mineral and metal biogenesis, formation of biomaterials, biomimetic strategies relevant to metallurgical processing and examples of minerals, and ore deposits formed due to biomineralization.

• Microbiological aspects of microorganisms encountered in acid mine drainage and bioleaching operations.

• Known mechanisms in microbe–mineral interactions. Bacterial attachment mechanisms to various mineral surfaces are highlighted. Electrochemical aspects are brought out. Metal-tolerance and use of preadapted microorganisms in bioleaching are illustrated with examples.

• History of biohydrometallurgy traced chronologically to bring out major developments in the area since ancient times to the present period. General methods adopted in biohydrometallurgical practices such as dump, heap, in situ and stirred tank leaching of ores and concentrates are discussed in detail. Advantages and disadvantages of various bioleaching technologies are highlighted from an engineering point of view.

• Bioleaching practices adopted for extraction of specific metals from their ores and concentrates are discussed with examples from copper, uranium, zinc, nickel, cobalt, and gold.

• Electrochemical principles and concepts play a major role in bioleaching processes since many sulfide minerals behave as electrodes in a leaching medium. Galvanic effects are very prominent in multimineral systems. Selective dissolution of active sulfide minerals (e.g., sphalerite, pyrrhotite, and pentlandite) can be brought about in presence of nobler minerals such as pyrite and chalcopyrite. Bioleaching reactions can also be controlled with respect to reaction rates under the influence of applied DC potentials and currents. A new process, termed, Electrobioleaching has been developed to achieve selective and rapid dissolution of desired sulfide mineral constituents from complex multisulfide ores and concentrates. Also, use of electrochemical bioreactors has been demonstrated to promote rapid growth of Acidithiobacillus ferrooxidans with reduced generation periods. Application of Electrobioleaching to sphalerite and chalcopyrite concentrates as well as to recover copper, nickel, and cobalt from ocean ferromanganese nodules is demonstrated.

• Microbially induced mineral beneficiation is an emerging area which has not been commercialized yet. As different from bioleaching, which involves bacterial oxidation and dissolution of minerals for metal extraction, biobeneficiation can be used to beneficiate as-mined ores with a view to removal of undesirable mineral impurities, thus enriching them with the desired mineral phase before metal extraction. Microbially induced flotation and flocculation of ores can be brought about through microbe–mineral interactions which render the mineral surfaces hydrophobic or hydrophilic through surface chemical alterations. Many mineral-specific bioreagents containing exopolysaccharides and proteinaceous compounds serve as flotation collectors and depressants as well as flocculants or dispersants. The use of biobeneficiation is demonstrated with relevance to beneficiation of iron ores, bauxite, clay, sulfide ores containing sphalerite, galena, chalcopyrite, pyrite, and arsenopyrite as well as various industrial minerals such as limestone, dolomite, and silica sands.

• Realizing the current novel developments in metals biotechnology, extended applications are illustrated with respect to reduction bioleaching, bioprocessing of rare-earth elements, bioprocessing of metallurgical wastes such as slags, tailings, fly-ash, flue dusts, used batteries, sludges, and spent catalysts. Bioprocessing of different electronic wastes has assumed great significance since they are treasures of multiple metals such as gold, silver, copper, rare earths, zinc, cadmium, nickel, and aluminum. Urban biomining of metals has become possible to tackle the generation of voluminous quantities of electronic wastes. Polymetallic sulfide ores, black schists as well as ocean nodules are potential sources of base and noble metals. Application of bioleaching to treat such complex resources has become relevant and commercially viable.

• Biofouling, biodeterioration, and microbially influenced corrosion constitute a significant area in metals biotechnology and metallurgical aspects of biofouling and resulting microbial corrosion of various metals and alloys are analyzed. Biodeterioration of cements and concretes as well as microbial corrosion of steel-reinforced concretes are illustrated.

• Similar to biofouling and microbial corrosion, generation of acid mine drainage is yet another deleterious consequence of microbial interactions with metals and minerals. Types and microbial aspects of acid mine drainage are illustrated with respect to involved microorganisms, mechanisms, tests for prediction of acid formation and prevention, and remediation methods. Case studies from commercial mining operations are outlined to bring out the practical significance of acid mine drainage and its remediation through biotechnology.

• For students, researchers, and professionals interested in the area of metals biotechnology, it becomes essential to familiarize with experimental and research methods and protocols. With this in mind, a complete chapter is devoted to experimental and research methods in metals biotechnology. Experimental protocols and procedures for isolation, identification, and enumeration of various microorganisms are illustrated. Bioleaching test methods are analyzed with respect to simulation of mining conditions. Similarly, research methods in mineral biobeneficiation, microbial corrosion, and evaluation of acid mine drainage are described.

References

1. Dunbar WS. Biotechnology and the mine of tomorrow. Trends Biotechnol. 2017;35:79–89.

2. Johnson DB. Biomining-biotechnologies for extracting and recovering metals from ores and waste materials. Curr Opin Biotechnol. 2014;30:24–31.

3. Banerjee I, Burrell B, Reed C, West AC, Banta S. Metals and minerals as a biotechnology feedstock: engineering biomining microbiology for bioenergy applications. Curr Opin Biotechnol. 2017;45:144–155.

4. Johnson DB. Development and application of biotechnologies in the metal mining industry. Environ Sci Pollut Res. 2013;20:7768–7776.

5. Nancharaiah YV, Mohan SV, Lens PNL. Biological and bioelectrochemical recovery of critical and scarce metals. Trends Biotechnol. 2016;34:137–155.

6. Zhuang WQ, Fitts JP, Ajo-Franklin CM, Maes S, Alvarez-Cohen L, Hennebel T. Recovery of critical metals using biometallurgy. Curr Opin Biotechnol. 2015;33:327–335.

Chapter 2

Biotechnology–Materials Interface

Biogenesis and Biomineralization

Abstract

Biotechnology–materials interface is outlined with respect to microbial synthesis of different minerals, metals, composite materials, and ceramics. Biology–metals cycle is illustrated in the light of consequences of microbe–mineral interactions related to biogenesis, biomineralization, bioleaching, biomaterials processing, environmental degradation, and bioremediation. Synthesis of various minerals by prokaryotes is illustrated with respect to biologically controlled and biologically induced mineralization along with examples from natural mineral formation. Microorganisms inhabiting iron ores, bauxite, clays, sulfide ores, limestone, ocean nodules, as well as gold-bearing ores are analyzed with respect to role of indigenous microbial habitats in the formation and conversion of minerals such as magnetite, hematite, bauxite, kaolinite, limestone, silica, chalcopyrite, galena, Sphalerite, pyrite, and metallic gold and platinum.

Beneficial aspects of microorganisms inhabiting the above ore deposits are brought out with respect to application of biotechnology in development of modern biomaterials, biomimetic strategies, bioleaching and microbially induced mineral beneficiation, and methods to combat biofouling, microbial corrosion, and environmental pollution.

Keywords

Biotechnology–materials interface; biomaterials; biomineralization; biogenesis; biogenic minerals

In this chapter, microbe–mineral–metal interactions are examined with respect to biogenesis of mineral deposits. Biomineralization processes are defined and classified in the light of formation and conversion of different oxide and sulfide minerals under the earth’s crust. Many types of microorganisms inhabit extreme and hostile mining environments promoting formation of different minerals and metals. Biosignatures of microbial–mineral interactions could be observed in many rocky mineral–laden deposits. In Fig. 2.1, bluish waters emanating and flowing from copper sulfide containing rocks from a copper mine could be seen. The bluish acidic solution is copper sulfate produced due to dissolution of the copper sulfide mineral brought about by the Acidithiobacillus group of bacteria inhabiting the rock surfaces. The role of Acidithiobacillus in the oxidation of sulfide minerals and in the generation of metal-laden acidic drainages is well known. In this chapter, biomineralization and biogenesis of various minerals forms are illustrated with respect to the following aspects.

• Biotechnology–materials interface

• Biomaterials and biomimetics

• Biomineralization processes and classification

• Biogenesis of iron ores, bauxite, sulfide minerals, and other ore deposits

Figure. 2.1 Biogenic copper sulfate formed through in situ oxidation by Acidithiobacillus spp.

It becomes essential to understand the types of and roles of various microorganisms inhabiting ore deposits before application of microbially mediated mineral extraction and environmental control processes are analyzed.

Biotechnology–Materials Interface

Interactions pertaining to biology–materials interface date back to several billions of years. Nucleosynthesis of materials in the stellar level dates back to almost 20 billion years. Nonbiotic materials processing by earth dates back to almost 4.5 billion years after which came biologically mediated processing of materials (about 3.5 billion years ago). In the cosmic scale of events, human efforts to synthesize materials are relatively new, coming only after stellar and microbiological processing. In this respect, one has to learn the art of metals and materials processing from the tiny microorganisms inhabiting earth and ocean floors. Microorganisms which bring about biogenesis, biomineralization, and biomaterials processing since more than billion years ago have undergone mutational and genetic changes to survive in extreme environments with respect to pH variations, oxygen availability, temperature fluctuations, and increased toxic metal concentrations. The organisms inhabiting the earth’s crust have evolved to process large quantities of valuable metals and minerals under extreme environmental conditions [1].

Biotechnology–materials cycle in nature involves biogenesis and biomineralization of ore deposits, dissolution of metals from minerals, biosynthesis of bulk engineering and composite materials, biofouling and microbial corrosion of metals as well as degradation and bioremediation of polluted environments. What had been produced and processed through biogenic reactions ultimately returns back as degraded and bioaccumulated products back to the earth, completing the biological cycle. A microbial cell functions as a fully automated modern micromill capable of different functions such as production of biopolymers, inter- and intracellular accumulation and sorption of metals and compounds, dissolution and corrosion of metals and minerals, as well as degradation and remediation of environment [1]. Material-processing capabilities of a microbial cell are illustrated in Fig. 2.2.

Figure. 2.2 Microbial cell with its potential functions.

Biology–materials interface include several materials- and minerals- related processes such as

• biomineralization and biogenesis;

• biomaterials processing (modern materials, metal–matrix and polymer–matrix composites, and ceramics);

• microbial extraction of metals (biohydrometallurgy);

• microbially mediated beneficiation to produce commercial quality ore minerals for metal production;

• biofouling, biodeterioration, and microbially influenced corrosion of metals and alloys;

• environmental degradation (acid mine drainage, for example); and

• bioremediation and environmental protection using microorganisms.

The above microbial processes and consequences are beneficial for the development of modern biotechnological processes. For example, an understanding of biogenesis and biomineralization of ore deposits under the earth’s crust and ocean floors will facilitate isolation and industrial use of many mining microorganisms to extract metals and synthesize modern bulk and nanomaterials. Bioindicators and biosensors to locate mineral and metal deposits can be developed. Advances in nanobiotechnology and the use of environmentally benign, cost-effective and energy-efficient bioreagents will pave the way for synthesis of modern strategic materials. Biohydrometallurgy and biobeneficiation processes are potential industrial strategies for environmentally benign production of industrial raw materials and finished metals. On the other hand, biofouling, biodeterioration, microbial corrosion of metals and alloys, and environmental pollution brought about by microbial activities are harmful consequences. Thanks to positive developments in environmental biotechnology, all the above deleterious consequences can be controlled and minimized to a greater extent. While several microorganisms are implicated in environmental pollution (acid mine drainage, for example), there exists in the same polluted environments, potential bioremediating organisms (e.g., sulfate-reducing bacteria; SRB) that can be harvested and utilized for detoxification of contaminated soils and waters.

Biomimetics and Biomaterials

Several minerals and metals can be termed as biogenic. Some classical examples include limestone (CaCO3) and silica (SiO2) formed since ancient times by activities of several microorganisms. Iron oxides such as magnetite (Fe3O4) are biogenic formed by interaction with anaerobes and magnetotactic bacteria. Most of sulfide, sulfate, and oxide minerals form part of bacterial cycles in nature. Among the metals, gold, silver, selenium, and tellurium are considered biogenic as also sulfur. Bacteria, fungi, algae, and plant species participate in mineral formation, conversion, and speciation. Mineral–metal–bacteria cycles in nature are important in geomicrobiology and biogeochemistry [2–4].

Simpler microorganisms such as bacteria and higher organisms like mollusks and plants participate in different types of biomineralization. Bacterial activity essentially involves surface binding of metal ions, oxidation–reduction, bioaccumulation, and precipitation, while higher organisms bring about synthesis of more structurally ordered materials. Synthesis of polymer–CaCO3 composites by mollusk shells is a classic example. Participation of ferritin—the protein shell containing channels to allow permeation of metal cations (such as iron and manganese) and anions such as sulfates, carbonates, and chlorides in the formation of biominerals such as magnetite, apatite, and manganic compounds is now recognized.

Bioprocessing of several engineering materials utilizing the principles of biomineralization can be achieved. Biomimetic materials processing is governed by three major aspects, namely [2,3]:

• mineral specificity,

• incremental net shape formation, and

• compartmentalized processing.

Reversed micelles and microemulsions are used to synthesize inorganic nanoparticles with controlled sizes and shapes. By sequential deposition strategies, high-density ceramics can be synthesized.

Biomineralization offers ample scope for novel developments in materials engineering. Organic supramolecular assemblies in biomaterial systems become relevant. Interfacing between molecular architecture and materials engineering through biomineralization and biomimetic strategies holds the key for the development of modern materials. Metals such as copper, iron, lead, and zinc can be deposited on bacterial cell walls in the form of sulfides, oxides, or carbonates. Biominerals are formed in well-defined intra- or intercellular sites. Organic and inorganic phases are involved in biomineralization. Both biologically controlled and induced processes may be involved with participation of bacterial proteins and enzymes. Biomineralization consists of discrete, self-assembled supramolecular parts such as vesicles and micelles, in a nanoscale. Four types of constructional processes are involved in biomineralization, namely, supramolecular preorganization, interfacial molecular recognition, vectorial regulation, and cellular processing [2–4].

Biomimetic material engineering involves bioconcepts, biosystems, and biomolecules. Nanoscale synthesis of materials involves strategies such as host–guest and ligand capping, while crystal engineering involves templating, directed growth, and microstructural fabrication. Biogenesis can be mimicked to construct special materials. For example, artificial polymerized vesicles can be designed to mimick biological functions. Colloidal gold, silver, and platinum and compounds such as metal sulfides, oxides, and chlorides can be synthesized in different shapes, sizes, and in crystalline or amorphous states for strategic applications [2–4].

Biomineralization and Biogenesis Relevant to Ore Deposits

Any discussion on biogenesis and biomineralization relevant to ore deposits raises the following questions.

• What types of microorganisms inhabit ore deposits?

• For what reasons and purposes the organisms inhabit ore deposits?

• What mineral-related functions they perform and bring about?

The synthesis of minerals by prokaryotes (bacteria and archaea) can be classified under [5, 6]

• Biologically controlled mineralization (BCM)

• Biologically induced mineralization (BIM)

Under BIM processes, minerals nucleate and extracellularly grow owing to metabolic activities of microorganisms and interaction with metabolic products. On the other hand, BCM is an organic matrix-mediated mineralization, wherein the minerals are deposited within or on organic matrices (vesicles) within the cell, making it possible for the microorganisms to exercise greater control over nucleation and growth. While mineral particles formed by BCM are structurally well ordered having close size distribution and exhibiting consistent crystal habits, those formed by biologically induced processes are generally characterized by poor crystallinity and having wider particle size distributions [5, 6].

Cell and exopolymer surfaces are important in BIM systems. Electrostatic adsorption of metal cations can occur on negatively charged cell and exopolymer surfaces. Both active and passive mineralization processes have been known. Nonspecific cation-binding along with solution anions resulting in surface nucleation and growth of mineral forms is referred to as passive mineralization, whereas direct redox transformation of surface-adsorbed metal ions facilitates active mineralization. Bacterial surface properties can be distinguished with respect to cell wall architecture of Gram-negative and Gram-positive bacteria. Cell walls of archaea are much different. BIM through passive surface-oriented processes include metal oxides such as hematite, goethite, metal phosphates and carbonates, and some metal sulfides. Active mineralization under BIM has many examples such as formation of iron sulfides by SRB [5, 6]. Some biologically induced iron and manganese minerals include goethite, ferrihydrite, magnetite, siderite, pyrite, pyrrhotite, jarosites, rhodochrosite, and birnessite.

Iron and manganese-oxidizing bacteria can precipitate both metal oxides under acidic and neutral pH conditions. Iron oxyhydroxides precipitation by A. ferrooxidans and Leptospirillum spp. through ferrous oxidation is well established. Mesophilic and thermophilic archaea such as Ferroplasma spp., Sulfolobus spp., and Acidianus brierleyi are well known iron oxidizers. Aerobic ferrous ion oxidization at neutral pH also occurs. Anaerobic ferrous ion oxidization through nitrate metabolism is known. Several Mn (II)-oxidizing bacteria such as Leptothrix and Pseudomonas spp. are also known.

List of some important minerals produced by biologically controlled and induced mineralization processes is given in Table 2.1 [7].

Table 2.1

Calcium-bearing minerals constitute of about 50% of known biominerals as calcium-containing phosphates, carbonates, and oxalates. Similarly, close to 20%–25% of such minerals are amorphous. Calcium carbonate is the most abundant, occurring as calcite, aragonite, and vaterite. Another 25% are phosphatic minerals, mostly produced by biocontrolled processes. Many of the biogenic minerals are hydrated. The iron biominerals are of great practical significance because they constitute approximately 40% of all minerals generated by microorganisms.

Biogenic minerals as different from inorganically produced minerals:

• possess unusual external morphologies and

• are usually composites or crystal agglomerates separated by organic matrix [7–10].

Different types of environments favorable for bacterially mediated mineral formation are illustrated [9]. A close link between microbiology, mineralogy, and geochemistry existing in a mining environment can be seen readily in sulfide ore tailings existing at mine sites. Waste mined over burden and processed ore tailings containing pyrite and sulfide minerals host microbial habitats, mainly acidophilic chemolithotrophs. Microbiology of such environments needs to be understood for developing effective bioremediation technologies. A dynamic relationship between aerobic and anaerobic organisms exists in many tailing storage sites. Different secondary minerals could also be formed due to activity of indigenous microorganisms. The cells provide nucleation sites for development of mineral forms. For example, in oxidizing zones, oxidized iron minerals can form, while in oxygen-depleted regions, reduced iron sulfides will be formed. Microbial activity can also lead to precipitation of iron sulfate, jarosites, and other mineral-based compounds.

In different mill tailings, hot springs and stream sediments, clay-like silicate minerals are found to be associated with bacterial cells. In some other cases, pure silica formation around bacterial cells has been observed. Bacterial surface layers encased in amorphous silica have been known. Bacterial cell surfaces can also biosorb silicate ions. Binding of silicate anions lead to subsequent deposition of silicate mineral phases which can further develop.

Microbialites are carbonaceous organo-sedimentary structures which exemplify mineralized microbial communities.

Sulfide Minerals

The sulfur–bacteria cycle contains interlinked reaction phases such as [11]

• dissimilatory sulfate reduction enabling organisms to synthesize sulfur-based amino acids for protein generation;

• degradation of protein and organic sulfur due to death of organisms facilitating release of free sulfides;

• dissimilatory sulfate reduction to yield H2S and sulfides;

• oxidation of sulfides to sulfur and sulfates.

The sulfur–bacteria cycle in a mining environment is represented in Fig. 2.3. Microorganisms involved in the sulfur cycle include

• Acidithiobacillus spp.,

• other lithotropic genera,

• Acidophilic and neutrophilic heterotrophs,

• photosynthetic bacteria of different types,

• facultative anaerobes, and

• Desulfovibrio, Desulfotomaculum, and Desulfuromonas spp.

Figure. 2.3 Sulfur–bacteria cycle in a mining environment.

Sulfides generated by sulfate reduction can be precipitated as metal sulfides in soil environments. Many sedimentary sulfide mineral deposits are formed due to such biomineralization processes. Sulfide deposits of copper, lead, and zinc along with iron sulfides (FeS2) are formed.

Laser ablation mass spectrometry of sulfur isotopic compositions showed that grains of pyrite formed almost 3.4 billion years ago in Barberton, South Africa due to bacterial reduction of seawater sulfate. Oceans were rich in sulfur and active SRB reduced them to precipitate pyrite in marine sediments [12]. SRB plays an important role in sedimentary environments to form sulfide minerals such as FeS2.

Laboratory evidence to support the biogenesis of metal sulfides of Sb, Bi, Fe, Co, Cd, Pb, Zn, and Ni has been reported in the presence of Desulfovibrio desulfuricans in a lactate containing broth culture. Models for biogenesis of sedimentary metal sulfides have been demonstrated using column experiments. The results demonstrated that biogenesis of large amounts of metal sulfides in a sedimentary environment is possible in the presence of higher concentrations of metals ions [13].

In the earth’s crust, indigenous microorganisms interact with minerals promoting their weathering. Physicochemical as well as redox states of various minerals could thus be altered. An example of a supergene copper deposit which has been influenced by microorganisms is Morenci copper mines in Arizona (The United States). A limonite-leached cover exists over an enriched chalcocite with intermittent covellite along with coatings on primary chalcopyrite and pyrite. Weathering and copper enrichment cycles occurred and leached out copper from the top, transported downward, and concentrating at depth. Organisms such as A. ferrooxidans attached to ore substrates can catalyze biogeochemical and sulfide/iron oxidation processes [10]. Copper enrichment can occur as

(2.1)

Also, SRB can also participate in precipitation and deposition of sulfide minerals. H2S formed due to anaerobic bacterial sulfate reduction may contribute to metal sulfide enrichment. An example cited is the sulfide enrichment in the Mike gold deposits in Carlin, Nevada (The United States). Similarly, microorganisms can solubilize uranium in uranium ore deposits facilitating their mobilization. Uraninite and coffinite from a sandstone deposit in Xinjiang, China are reported to be precipitated by microorganisms [10].

Iron Ores

Biogenic iron oxides display intimate association with microorganisms inhabiting the ore deposits. In natural sediments, iron oxide particulates are found to occur in close proximity to bacterial cell walls containing extracellular biogenic iron oxides and various biopolymers. Iron-oxidizing and iron-reducing bacteria colonize the biofilms formed on many iron oxide minerals [14–20].

Several types of microorganisms growing under extreme environments altering between acidic to neutral pH, aerobic and anaerobic, as well as mesophilic and thermophilic conditions are capable of microbial oxidation of ferrous iron and reduction of ferric iron.

Some examples are Acidithiobacillus sp., Gallionella sp., Leptothrix sp., Leptospirillum sp., and Thermoplasmales (archea). Leptothrix spp. can form FeOOH sheaths around iron oxide minerals through production of exopolysaccharides as a protection mechanism.

Extracellular biopolymers such as high molecular weight polysaccharides and proteinaceous compounds are produced by several iron bacteria such as Bacillus spp. and Magnetotactic bacteria.

Ancient biogenic iron minerals contain biosignatures as in banded iron formations (BIF). Nanocrystals of lepidocrocite on and away from the cell wall of Bacillus subtilis have been observed due to ferrous iron oxidation. Diverse group of Gram-negative prokaryotes such as Vibrio, Cocci, and Spirillum constitute magnetotactic bacteria which synthesize intra- and intercellular magnetic minerals (such as magnetite) and magnetosomes. Several magnetotactic bacteria (living under aerobic and anaerobic conditions) and their magnetosomes have been isolated and characterized from the Tieshan iron ore deposits in China [17]. Microbially induced iron ore formation has been confirmed at Gunma iron ore mine, Japan [21].

Ubiquitous microorganisms inhabiting iron ore deposits are useful in iron ore beneficiation (e.g., removal of alkalis, silica, clays, phosphorous, and alumina). Because the presence of phosphorous in the iron ore promotes bacterial growth (as an energy source), iron oxide particles having higher phosphorous contents were seen to be colonized by different bacterial cells. Microbial phosphorous mobilization in iron ores has been reported. A polymer-producing bacterium (B. caribensis) has been isolated from a high phosphorous Brazilian iron ore [19]. Microorganisms such as Acidithiobacillus, Clavibacter, and Aspergillus isolated from iron ores are good phosphate solubilizers, because they generate inorganic and organic acids.

Shewanella oneidensis, an iron-reducing bacterium which produces mineral-specific proteins exhibit surface affinity towards goethite under anaerobic conditions. S. oneidenisis are capable of recognizing (sensing) goethite under anaerobic conditions. Shewanella sp. prefers FeOOH and not AlOOH. Such a preferential microbial–mineral affinity could be beneficially used to separate alumina, gibbsite, and aluminum silicates (clays) from iron oxides. Microbially secreted proteins are involved in metal reduction. Protein secretion and transport as well as biosynthesis of exopolysaccharides are very important and useful in iron ore transformation. Shewanella putrefaciens, a facultative anaerobic, Gram-negative bacterium can reduce ferric iron oxides and attach preferentially to magnetite and ferrihydrite. Enhanced adhesion of phosphate-utilizing organisms on iron oxides promotes formation of iron phosphate complexes [17, 18].

Magnetite particles formed by dissimilatory, extracellular iron reduction are generally poorly crystallized. Ferrous ions can react with excess ferric oxyhydroxides to form mixed Fe (II) and Fe (III) oxides as magnetite.

BIM of magnetite has been possible in the presence of cultures of Shewanella and Geobacter. Possibility of intracellular deposition of minerals also exists. For example, intracellular iron sulfide formation within cells of SRB such as Desulfovibrio and Desulfotomaculum species has been reported [22–24].

Biomineralization brought out by prokaryotes has practical significance in environmental ore deposit formation, mineral exploration through biomarkers, and also in bioremediation of metal-contaminated waters and soils. For example, formation of extensive Precambrian BIF has been attributed to iron-oxidizing bacteria. Biologically formed minerals may be useful as bioindicators on earth and ocean floors.

An example of BCM is the generation of magnetic minerals by Magnetotactic bacteria. Two types of such bacteria are often mentioned, namely, iron oxide—types which mineralize magnetite (Fe3O4) and the iron sulfide—types which mineralize greigite (Fe3S4) [25].

BIF are the largest iron sources distributed globally dating back to about 4 billion years. They contain up to 50% silica and between 20% and 40 % iron and are sedimentary in origin. Main iron minerals such as hematite and magnetite found in BIF are considered to be of secondary origin. Earlier categorization showed domination of carbonates such as siderite and ankerite. It is likely that different mechanisms might have prevailed in BIF [26].

One traditional model assumed the oxidation of hydrothermal Fe (II) through biotic and abiotic oxidation. Microfossils found in Australia suggested the existence of Cyanobacteria which display various potential biomarker molecules. The presence of oxygen also has been found from the composition of rocks. Formation of ferric iron oxides without oxygen, involving photo-oxidation of ferrous iron by UV radiation has also been suggested. Another recent hypothesis offers direct biological Fe (II) oxidation by anoxygenic phototrophic bacteria.

The presence and nature of minerals of primary and secondary origin in BIF have been widely analyzed. The presence of iron phases such as magnetite, ferrosilicates, siderite, ankerite, and pyrite needs to be considered. Secondary origins of magnetite have been described. Magnetite could have been formed when microbially reduced ferrous iron reacted with initial ferric oxyhydroxides. Oxidation of siderite could also have occurred.

(2.2)

(2.3)

(2.4)

(2.5)

Several theories have been proposed.

Layering of silica-carbonate–rich and iron-rich bands is characteristic of BIF.

Biomineralization of Bauxites

Microbial communities ubiquitously present in ore deposits can dissolve and precipitate rock-forming minerals. The presence of various microorganisms in gray-colored bauxites and zones of transition between red and gray bauxites along faults has been validated. Mobility and redox control of different metals such as iron, chromium, manganese, and vanadium with relevance to bauxite mineralization are brought about by bacteria. Pyritized bauxite deposits contain sulfur and iron-oxidizing and reducing microbes. Intimate association of microorganisms with pyrite/siderite and goethite/hematite mineralization in many bauxite deposits are indicative of bacterially controlled redox reactions. Microbial cells adhere to mineral surfaces and grow as biofilms altering the redox chemistry, creating aerobic and anaerobic zones [27, 28].

Both microbial and chemical weathering of silicates can occur in bauxite deposits. Variations between highly oxidized environments to gradual reducing conditions are observed during the evolution of bauxites brought out by microorganisms. Organic carbon, sulfur, iron, and moisture present in bauxites can be used as energy sources by ubiquitous microbes. Role of different microorganisms in the formation and transition of bauxite minerals has been understood [27, 28]. Different stages involved in bauxite biomineralization under redox conditions can be related to rock weathering as a result of interaction with organic and inorganic microbial metabolic products. Release of iron, silicon, and aluminum and precipitation of biogenic sulfides, carbonates, and iron oxides can occur by biological weathering, as also, sulfate formation and sulfide precipitation by aerobic and anaerobic microbial processes. Microbial communities in bauxite ore deposits can dissolve primary rock-forming minerals and also could provide nucleation sites for the formation of secondary minerals. Transformation stages in bauxites may involve ferric iron reduction facilitating pyrite formation and subsequent oxidation to goethite. Pyrite having different morphological features is found to be generally associated with fossilized bacteria in gray–red bauxite. Occurrence of fine-grained spherical pyrite and pyrite pseudomorphs after iron oxides indicates that pyrite formation is a consequence of bacterial interactions.

Involvement of different microbes in bauxite mineralization can be understood with respect to bacterial metabolism facilitating redox reactions with different metals and sulfur species, biocatalysis involving selective oxidation and reduction of metals and precipitation of secondary minerals, role of aerobes and anaerobes in redox reactions, as well as distribution and remobilization of minerals in the presence of bacterial consortia.

Different autotrophic and heterotrophic bacteria, fungi, and yeasts were isolated from some Western Indian bauxite deposits as shown in Table 2.2 [29]. Role of isolated organisms in biomineralization processes is outlined. Acidithiobacillus spp. produce sulfuric acid containing ferric ions, and the pH changes can facilitate weathering of aluminosilicates and precipitation of iron oxyhydroxides and silicate minerals. Biological and chemical weathering causes mobilization and sedimentation of alumina in swamps, where it can be converted to alumino-oxyhydroxides. Bacillus spp. can promote the release of alkaline metals such as sodium, potassium, and calcium. Magnesium and iron released from bauxites can be reprecipitated through microbial processes. Aluminum and silica essentially remain in the matrix contributing to bauxite mineralization. Cladosporium fungi are capable of iron reduction and dissolution of alumina, while Pseudomonas spp. can anaerobically reduce ferric oxides. Bacteria such as Paenibacillus polymyxa and Bacillus coagulans, through the excretion of exopolysaccharides can flocculate iron oxides, alumina, and calcite, altering their distribution in the bauxite matrix. All the above bauxite-inhabiting microbes synergistically participate in different redox reactions leading to the formation of biogenic bauxite deposits. Participation of microorganisms in weathering of bauxitic deposits has been suggested by many authors. The role of SRB in the weathering of aluminosilicates has been suggested.

Table 2.2