Manganese biomining: A review

Biomining comprises of processing and extraction of metal from their ores and concentrates using microbial techniques. Currently this is used by the mining industry to extract copper, uranium and gold from low grade ores but not for low grade manganese ore in industrial scale. The study of microbial genomes, metabolites and regulatory pathways provide novel insights to the metabolism of bioleaching microorganisms and their synergistic action during bioleaching operations. This will promote understanding of the universal regulatory responses that the biomining microbial community uses to adapt to their changing environment leading to high metal recovery. Possibility exists of findings ways to imitate the entire process during industrial manganese biomining endeavor. This paper reviews the current status of manganese biomining research operations around the world, identifies factors that drive the selection of biomining as a processing technology, describes challenges in exploiting these innovations, and concludes with a discussion of Mn biomining’s future.     

Genomics, metagenomics and proteomics in biomining microorganisms

The use of acidophilic, chemolithotrophic microorganisms capable of oxidizing iron and sulfur in industrial processes to recover metals from minerals containing copper, gold and uranium is a well established biotechnology with distinctive advantages over traditional mining. A consortium of different microorganisms participates in the oxidative reactions resulting in the extraction of dissolved metal values from ores. Considerable effort has been spent in the last years to understand the biochemistry of iron and sulfur compounds oxidation, bacteria-mineral interactions (chemotaxis, quorum sensing, adhesion, biofilm formation) and several adaptive responses allowing the microorganisms to survive in a bioleaching environment. All of these are considered key phenomena for understanding the process of biomining. The use of genomics, metagenomics and high throughput proteomics to study the global regulatory responses that the biomining community uses to adapt to their changing environment is just beginning to emerge in the last years. These powerful approaches are reviewed here since they offer the possibility of exciting new findings that will allow analyzing the community as a microbial system, determining the extent to which each of the individual participants contributes to the process, how they evolve in time to keep the conglomerate healthy and therefore efficient during the entire process of bioleaching.     

The use of genetic probes to detect microorganisms in biomining operations

Summary Microorganisms are currently used for the recovery of copper from mining dumps of low-grade ore. One of the most important microorganisms involved in copper-solubilization isThiobacillus ferrooxidans, although many other microbial genera are also thought to be implicated. A mining dump poses some special problems for the industrial microbiologist because it represents a non-sterile and heterogeneous substrate. Consequently, to enhance our knowledge of the role of microorganisms in metal recovery we must identify the indigenous microorganisms and understand their respective contributions to the process. In addition, when a superior strain of microorganism is developed in the laboratory, by genetic engineering or by other means, we must have a method to evaluate the maintenance of such a strain in the mining dump. In this paper, we describe DNA homology studies, using dot blot and Southern blot analysis of hybridizations of both whole genomic DNA and cloned DNA sequences, to identify and enumerate several bioleaching microorganisms. We demonstrate that it is possible to identify different species of microorganisms and, in one case, to discriminate between different strains of a single species. It is also possible to identify and quantitate certain species in a mixed culture. DNA hybridization analysis has several advantages over the more conventional bacteriological methods of identification, especially in a complex bioleaching situation.     

Metabolic modelling and flux analysis of microorganisms from the Atacama Desert used in biotechnological processes

Metabolic modelling is a useful tool that enables the rational design of metabolic engineering experiments and the study of the unique capabilities of biotechnologically important microorganisms. The extreme abiotic conditions of the Atacama Desert have selected microbial diversity with exceptional characteristics that can be applied in the mining industry for bioleaching processes and for production of specialised metabolites with antimicrobial, antifungal, antiviral, antitumoral, among other activities. In this review we summarise the scientific data available of the use of metabolic modelling and flux analysis to improve the performance of Atacama Desert microorganisms in biotechnological applications.     

A review of biotechnology processes applied for manganese recovery from wastes

The global consumption of manganese is rising due to its growing industrial requirement while the natural reserves of manganese are diminishing at an alarming rate. Consequently, recovery of manganese from metal containing wastes has become highly crucial. Bioleaching of metal from wastes using microbes provides an adequate advantage over the traditional method of recovery. A molecular level understanding of microbial catalyzed manganese recovery is essential for the exploitation of novel microorganisms for similar applications. In current scenario, the application of bioleaching concentrates on cost effective and eco-friendly recovery of precious metals from mining and industrial wastes. This review encompasses the modern improvements in biomining, highlights the comprehensive factors that emphasize the selection of manganese recovery technique, shed insights into spectacular progress in developing molecular based technologies and also identifies the applicability of different models in metal bioremediation which will not only aid in pollution abatement but also in the prevention of occupational health disorder.     

Solid-state fermentation

Solid-state fermentation has emerged as a potential technology for the production of microbial products such as feed, fuel, food, industrial chemicals and pharmaceutical products. Its application in bioprocesses such as bioleaching, biobeneficiation, bioremediation, biopulping, etc. has offered several advantages. Utilisation of agro-industrial residues as substrates in SSF processes provides an alternative avenue and value-addition to these otherwise under- or non-utilised residues. Today with better understanding of biochemical engineering aspects, particularly on mathematical modelling and design of bioreactors (fermenters), it is possible to scale up SSF processes and some designs have been developed for commercialisation. It is hoped that with continuity in current trends, SSF technology would be well developed at par with submerged fermentation technology in times to come.     

Life in blue: Copper resistance mechanisms of bacteria and Archaea used in industrial biomining of minerals

Industrial biomining processes to extract copper, gold and other metals involve the use of extremophiles such as the acidophilic Acidithiobacillus ferrooxidans (Bacteria), and the thermoacidophilic Sulfolobus metallicus (Archaea). Together with other extremophiles these microorganisms subsist in habitats where they are exposed to copper concentrations higher than 100 mM. Herein we review the current knowledge on the Cu-resistance mechanisms found in these microorganisms. Recent information suggests that biomining extremophiles respond to extremely high Cu concentrations by using simultaneously all or most of the following key elements: 1) a wide repertoire of Cu-resistance determinants; 2) duplication of some of these Cu-resistance determinants; 3) existence of novel Cu chaperones; 4) a polyP-based Cu-resistance system, and 5) an oxidative stress defense system. Further insight of the biomining community members and their individual response to copper is highly relevant, since this could provide key information to the mining industry. In turn, this information could be used to select the more fit members of the bioleaching community to attain more efficient industrial biomining processes.     

Bioleaching review part B:

This review describes the historical development and current state of metals leaching and sulfide mineral biooxidation by the minerals industries. During the past 20 years commercial processes employing microorganisms for mineral recovery have progressed from rather uncontrolled copper dump leaching to mineral oxidation and leaching in designed bioheaps for oxidation of refractory gold ores and for copper recovery. Also during this period of time, stirred tank bioleaching has been commercialized for cobalt recovery and for biooxidation of refractory gold ores. Chalcopyrite bioleaching in stirred tanks is on the verge of commercialization. Commercial applications of biohydrometallurgy have advanced due to favorable process economics and, in some cases, reduced environmental problems compared to conventional metal recovery processes such as smelting. Process development has included recognition of the importance of aeration of bioheaps, and improvements in stirred tank reactor design and operation. Concurrently, knowledge of the key microorganisms involved in these processes has advanced, aided by advances in molecular biology to characterize microbial populations.     

Maßgeschneiderte Mikroorganismen

Tailor‐made microorganisms Microbial diversity provides unlimited resources for the development of novel industrial processes and products. Since the beginning of the 20th century microorganisms have been successfully applied for the large scale production of bio‐based products. In recent years, modern methods of strain development and Synthetic Biology have enabled biotech engineers to design even more sophisticated and tailor‐made microorganisms. These microbes serve industrial processes for the production of bulk chemicals, enzymes, polymers, biofuels as well as plant‐derived ingredients such as Artemisinin in an ecologically and economically sustainable and attractive fashion. In the future, production of advanced biofuels, microbial fuel cells, CO₂ as feedstock and microbial cellulose are research topics as well as challenges of global importance. Continuous efforts in microbiology and biotechnology research will be pivotal for white biotechnology to gain more momentum in transforming the chemical industry towards a knowledge based bio‐economy.     

Identification of trehalose as a compatible solute in different species of acidophilic bacteria

The major industrial heap bioleaching processes are located in desert regions (mainly Chile and Australia) where fresh water is scarce and the use of resources with low water activity becomes an attractive alternative. However, in spite of the importance of the microbial populations involved in these processes, little is known about their response or adaptation to osmotic stress. In order to investigate the response to osmotic stress in these microorganisms, six species of acidophilic bacteria were grown at elevated osmotic strength in liquid media, and the compatible solutes synthesised were identified using ion chromatography and MALDI-TOF mass spectrometry. Trehalose was identified as one of, or the sole, compatible solute in all species and strains, apart from Acidithiobacillus thiooxidans where glucose and proline levels increased at elevated osmotic potentials. Several other potential compatible solutes were tentatively identified by MALDITOF analysis. The same compatible solutes were produced by these bacteria regardless of the salt used to produce the osmotic stress. The results correlate with data from sequenced genomes which confirm that many chemolithotrophic and heterotrophic acidophiles possess genes for trehalose synthesis. This is the first report to identify and quantify compatible solutes in acidophilic bacteria that have important roles in biomining technologies.     

Microbial leaching of metals from solid industrial wastes

Biotechnological applications for metal recovery have played a greater role in recovery of valuable metals from low grade sulfide minerals from the beginning of the middle era till the end of the twentieth century. With depletion of ore/minerals and implementation of stricter environmental rules, microbiological applications for metal recovery have been shifted towards solid industrial wastes. Due to certain restrictions in conventional processes, use of microbes has garnered increased attention. The process is environmentally-friendly, economical and cost-effective. The major microorganisms in recovery of heavy metals are acidophiles that thrive at acidic pH ranging from 2.0–4.0. These microbes aid in dissolving metals by secreting inorganic and organic acids into aqueous media. Some of the well-known acidophilic bacteria such as Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, Leptospirillum ferrooxidans and Sulfolobus spp. are well-studied for bioleaching activity, whereas, fungal species like Penicillium spp. and Aspergillus niger have been thoroughly studied for the same process. This mini-review focuses on the acidophilic microbial diversity and application of those microorganisms toward solid industrial wastes.     

Lessons from the genomes of extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms

This mini-review describes the current status of recent genome sequencing projects of extremely acidophilic microorganisms and highlights the most current scientific advances emerging from their analysis. There are now at least 56 draft or completely sequenced genomes of acidophiles including 30 bacteria and 26 archaea. There are also complete sequences for 38 plasmids, 29 viruses, and additional DNA sequence information of acidic environments is available from eight metagenomic projects. A special focus is provided on the genomics of acidophiles from industrial bioleaching operations. It is shown how this initial information provides a rich intellectual resource for microbiologists that has potential to open innovative and efficient research avenues. Examples presented illustrate the use of genomic information to construct preliminary models of metabolism of individual microorganisms. Most importantly, access to multiple genomes allows the prediction of metabolic and genetic interactions between members of the bioleaching microbial community (ecophysiology) and the investigation of major evolutionary trends that shape genome architecture and evolution. Despite these promising beginnings, a major conclusion is that the genome projects help focus attention on the tremendous effort still required to understand the biological principles that support life in extremely acidic environments, including those that might allow engineers to take appropriate action designed to improve the efficiency and rate of bioleaching and to protect the environment.     

Bioremediation of copper-contaminated soils by bacteria

Although copper (Cu) is an essential micronutrient for all living organisms, it can be toxic at low concentrations. Its beneficial effects are therefore only observed for a narrow range of concentrations. Anthropogenic activities such as fungicide spraying and mining have resulted in the Cu contamination of environmental compartments (soil, water and sediment) at levels sometimes exceeding the toxicity threshold. This review focuses on the bioremediation of copper-contaminated soils. The mechanisms by which microorganisms, and in particular bacteria, can mobilize or immobilize Cu in soils are described and the corresponding bioremediation strategies—of varying levels of maturity—are addressed: (i) bioleaching as a process for the ex situ recovery of Cu from Cu-bearing solids, (ii) bioimmobilization to limit the in situ leaching of Cu into groundwater and (iii) bioaugmentation-assisted phytoextraction as an innovative process for in situ enhancement of Cu removal from soil. For each application, the specific conditions required to achieve the desired effect and the practical methods for control of the microbial processes were specified.     

Linking ecology with economy: Insights into polyhydroxyalkanoate‐producing microorganisms

Polyhydroxyalkanoates (PHA) constitute a group of microbial biopolyesters with important ecosystem functions and a high biotechnological potential. During the past decade, the rapid development of new molecular and microscopic techniques resulted in novel insights into the ecology of PHA‐producing bacteria in aquatic and terrestrial microenvironments. Ecosystems showing fluctuating availability of carbon or transient limitation of essential nutrients, e.g. the rhizosphere of plants or estuarine sediments, contain a broad number of various PHA producers. PHA‐producing microorganisms show a widespread phylogenetic diversity and are often characterized by a symbiotic or syntrophic life style. PHA are already produced commercially in large‐scale fermentation. However, they have to compete economically with petrol‐based polymers. Hence, the development of low‐cost production strategies on the basis of diverse renewable materials is a crucial challenge. Ecological knowledge is required for these developments, which links both parts of the review together. The article highlights how a better understanding of the ecology of PHA‐producing microorganisms can lead to a broader application of microbial biopolymers on the basis of sustainable production processes. These processes have to be evaluated by means of life cycle assessment and Cleaner Production studies prior to their industrial implementation.     

Effects of key parameters in recycling of metals from petroleum refinery waste catalysts in bioleaching process

Environmental laws concerning spent catalysts disposal have become increasingly more severe in recent years. Due to the toxic nature of spent catalysts, their disposal can pollute the environment. The recovery of heavy metals decreases the environmental impact of the waste catalysts and the recycled product can be further used for industrial purposes. Bio-hydrometallurgical approaches, such as bioleaching, appear to offer good prospects for recovering valuable metals from spent refinery catalysts. Currently, identifying and modifying the parameters that influenced the efficiency of bioleaching is important for industrial sector. The biological system can be further improved through optimizing the bioleaching parameters, such as the nutrient culture media, amount of oxygen and carbon dioxide, pH, temperature, inoculum, metal resistance of microorganisms, chemistry of solid waste, particle size of solid waste, solid liquid ratio, bioleaching period, size of substrate, shaking speed, and also the development of more effective bioleaching microorganisms. In our previous review (Asghari et al. in J Ind Eng Chem 19:1069–1081, 2013), information available in the literature on the bioleaching fundamentals of spent catalysts with a focus on recent developments was reviewed in detail. In this study, the effects of most important factors that influence an efficient bioleaching process of spent refinery catalysts with the hope that these valuable and useful data can help determine the most efficient process will be discussed. The details of metals recovery with a focus on the effects of different variables in the bioleaching such as reaction time, pulp density, initial pH, particle size, nutrient concentration, temperature and buffer will also be presented.     

An Immunological Assay for Detection and Enumeration of Thermophilic Biomining Microorganisms

A specific, fast, and sensitive nonradioactive immunobinding assay for the detection and enumeration of the moderate thermophile Thiobacillus caldus and the thermophilic archaeon Sulfolobus acidocaldarius was developed. It employs enhanced chemiluminescence or peroxidase-conjugated immunoglobulins in a dot or slot blotting system and is very convenient for monitoring thermophilic bioleaching microorganisms in effluents from industrial bioleaching processes.     

Significance of microbial interactions in control of microbial ecosystems

A microbial ecosystem represents a delicately balanced population of microorganisms each interacting with and influencing the other members of the population. An understanding of the nature and effects of these interactions is essential to improving the performance of these ecologies, which are important, in such diverse processes as biological waste treatment procedures, water pollution abatement, industrial fermentations, human or animal digestives processes and in soil. There are several types of mocrobial interactions, such as commensalism, inhibition, food competition, predation, parasitism, and synergism, which either singly or in combination may influence the functioning of the microbial ecology. To understand interactions, it is necessary to perform a detailed study of the physiology of the individual predominating microorganisms to establish their requirements with respect to such environmental factors as nutrients, temperature, pH, oxidation-reduction potential, removal of waste products, or toxic materials which may be involved in control processes and to determine how these factors affect their capabilities. The sum total of this information will indicate the possible interactions between the microorganisms and will form the basis for conducting experiments either in the laboratory or with mathematical models. Such experiments will lead to an understanding of microbial activities and to the formulation of control measures, often using an alteration of the environmental factors for regulation of the microbial ecologies. Extensive research remains to be done on the microbial interact inns in obtain the desired, precise control of these ecological processes.     

极端嗜酸硫杆菌高密度培养的研究进展

极端嗜酸硫杆菌属微生物在生物冶金、生物脱硫以及固体废弃物的处置中扮演重要作用,但该类微生物在培养过程中细胞浓度很低,限制了该类微生物的广泛应用。高密度培养是提高微生物生产效率的有效手段。高密度培养技术在嗜酸微生物中的应用能够显著减少微生物培养的生成成本,缩短生产周期,极端嗜酸硫杆菌微生物菌剂的输出速率。本文从菌种选育、培养条件、培养方式综述了极端嗜酸硫杆菌高密度培养的研究现状。     

Integrative computational approach for genome-based study of microbial lipid-degrading enzymes

Lipid-degrading or lipolytic enzymes have gained enormous attention in academic and industrial sectors. Several efforts are underway to discover new lipase enzymes from a variety of microorganisms with particular catalytic properties to be used for extensive applications. In addition, various tools and strategies have been implemented to unravel the functional relevance of the versatile lipid-degrading enzymes for special purposes. This review highlights the study of microbial lipid-degrading enzymes through an integrative computational approach. The identification of putative lipase genes from microbial genomes and metagenomic libraries using homology-based mining is discussed, with an emphasis on sequence analysis of conserved motifs and enzyme topology. Molecular modelling of three-dimensional structure on the basis of sequence similarity is shown to be a potential approach for exploring the structural and functional relationships of candidate lipase enzymes. The perspectives on a discriminative framework of cutting-edge tools and technologies, including bioinformatics, computational biology, functional genomics and functional proteomics, intended to facilitate rapid progress in understanding lipolysis mechanism and to discover novel lipid-degrading enzymes of microorganisms are discussed.     

响应面法优化Fe~(2+)的微生物氧化条件

氧化亚铁钩端螺旋菌(Leptospirillum ferrooxidans,L.f)是一种极端嗜酸,专性自养氧化铁的细菌,能够耐受较低pH和较高的温度,被广泛应用于生物浸矿和环境治理。氧化亚铁钩端螺旋体菌的生物浸矿效率与其对Fe~(2+)氧化速率相关,因此,本文采用响应面法,通过建立二次多项式回归方程考察pH、温度、Fe~(2+)浓度及转速四个培养因素对Fe~(2+)氧化速率的影响。结果显示在pH为2.25、温度为32℃、初始Fe~(2+)浓度为175.36 mmol/L、转数为165 r/min时,Fe~(2+)最高氧化速率为0.2911 g/Lh。