Evaluation of Leptospirillum ferrooxidans for Leaching

Chalcopyrite bioleaching efficacy by extremely thermoacidophilic archaea leverages balanced iron and sulfur biooxidation

Factors that contribute to optimal chalcopyrite bioleaching by extremely thermoacidophilic archaea were examined for ten species belonging to the order Sulfolobales from the genera Acidianus (A. brierleyi), Metallosphaera (M. hakonensis, M. sedula, M. prunae), Sulfuracidifex (S. metallicus, S. tepriarius), Sulfolobus (S. acidocaldarius), Saccharlobus (S. solfataricus) and Sulfurisphaera (S. ohwakuensis, S. tokodaii). Only A. brierleyi, M. sedula, S. metallicus, S. tepriarius, S. ohwakuensis, and S. tokodai exhibited significant amounts of bioleaching and were investigated further. At 70-75 °C, Chalcopyrite loadings of 10 g/l were leached for 21 days during which pH, redox potential, planktonic cell density, iron concentrations and sulfate levels were monitored, in addition to copper mobilization. S. ohwakuensis proved to be the most prolific bioleacher. This was attributed to balanced iron and sulfur oxidation, thereby reducing by-product (e.g., jarosites) formation and minimizing surface passivation. Comparative genomics suggest markers for bioleaching potential, but the results here point to the need for experimental verification.

Microbial community structure in an uranium-rich acid mine drainage site: implication for the biogeochemical release of uranium

The generation of acid mine drainage (AMD) characterized by high acidity and elevated levels of toxic metals primarily results from the oxidation and dissolution of sulfide minerals facilitated by microbial catalysis. Although there has been significant research on microbial diversity and community composition in AMD, as well as the relationship between microbes and heavy metals, there remains a gap in understanding the microbial community structure in uranium-enriched AMD sites. In this paper, water samples with varying levels of uranium pollution were collected from an abandoned stone coal mine in Jiangxi Province, China during summer and winter, respectively. Geochemical and high-throughput sequencing analyses were conducted to characterize spatiotemporal variations in bacterial diversity and community composition along pollution groups. The results indicated that uranium was predominantly concentrated in the AMD of new pits with strong acid production capacity, reaching a peak concentration of 9,370 μg/L. This was accompanied by elevated acidity and concentrations of iron and total phosphorus, which were identified as significant drivers shaping the composition of bacterial communities, rather than fluctuations in seasonal conditions. In an extremely polluted environment (pH < 3), bacterial diversity was lowest, with a predominant presence of acidophilic iron-oxidizing bacteria (such as Ferrovum), and a portion of acidophilic heterotrophic bacteria synergistically coexisting. As pollution levels decreased, the microbial community gradually evolved to cohabitation of various pH-neutral heterotrophic species, ultimately reverting back to background level. The pH was the dominant factor determining biogeochemical release of uranium in AMD. Acidophilic and uranium-tolerant bacteria, including Ferrovum, Leptospirillum, Acidiphilium, and Metallibacterium, were identified as playing key roles in this process through mechanisms such as enhancing acid production rate and facilitating organic matter biodegradation.

Progress in bioleaching: fundamentals and mechanisms of microbial metal sulfide oxidation - part A

Abstract

Bioleaching of metal sulfides is performed by diverse microorganisms. The dissolution of metal sulfides occurs via two chemical pathways, either the thiosulfate or the polysulfide pathway. These are determined by the metal sulfides’ mineralogy and their acid solubility. The microbial cell enables metal sulfide dissolution via oxidation of iron(II) ions and inorganic sulfur compounds. Thereby, the metal sulfide attacking agents iron(III) ions and protons are generated. Cells are active either in a planktonic state or attached to the mineral surface, forming biofilms. This review, as an update of the previous one (Vera et al., 2013a), summarizes some recent discoveries relevant to bioleaching microorganisms, contributing to a better understanding of their lifestyle. These comprise phylogeny, chemical pathways, surface science, biochemistry of iron and sulfur metabolism, anaerobic metabolism, cell–cell communication, molecular biology, and biofilm lifestyle. Recent advances from genetic engineering applied to bioleaching microorganisms will allow in the future to better understand important aspects of their physiology, as well as to open new possibilities for synthetic biology applications of leaching microbial consortia.

Key points

• Leaching of metal sulfides is strongly enhanced by microorganisms

• Biofilm formation and extracellular polymer production influences bioleaching

• Cell interactions in mixed bioleaching cultures are key for process optimization

Discovery of ancestral L-ornithine and L-lysine decarboxylases reveals parallel, pseudoconvergent evolution of polyamine biosynthesis

Polyamines are fundamental molecules of life, and their deep evolutionary history is reflected in extensive biosynthetic diversification. The polyamines putrescine, agmatine, and cadaverine are produced by pyridoxal 5'-phosphate-dependent L-ornithine, L-arginine, and L-lysine decarboxylases (ODC, ADC, LDC), respectively, from both the alanine racemase (AR) and aspartate aminotransferase (AAT) folds. Two homologous forms of AAT-fold decarboxylase are present in bacteria: an ancestral form and a derived, acid-inducible extended form containing an N-terminal fusion to the receiver-like domain of a bacterial response regulator. Only ADC was known from the ancestral form and limited to the Firmicutes phylum, whereas extended forms of ADC, ODC, and LDC are present in Proteobacteria and Firmicutes. Here, we report the discovery of ancestral form ODC, LDC, and bifunctional O/LDC and extend the phylogenetic diversity of functionally characterized ancestral ADC, ODC, and LDC to include phyla Fusobacteria, Caldiserica, Nitrospirae, and Euryarchaeota. Using purified recombinant enzymes, we show that these ancestral forms have a nascent ability to decarboxylate kinetically less preferred amino acid substrates with low efficiency, and that product inhibition primarily affects preferred substrates. We also note a correlation between the presence of ancestral ODC and ornithine/arginine auxotrophy and link this with a known symbiotic dependence on exogenous ornithine produced by species using the arginine deiminase system. Finally, we show that ADC, ODC, and LDC activities emerged independently, in parallel, in the homologous AAT-fold ancestral and extended forms. The emergence of the same ODC, ADC, and LDC activities in the nonhomologous AR-fold suggests that polyamine biosynthesis may be inevitable.

Iron-Fueled Life in the Continental Subsurface: Deep Mine Microbial Observatory, South Dakota, USA

Iron-bearing minerals are key components of the Earth's crust and potentially critical energy sources for subsurface microbial life. The Deep Mine Microbial Observatory (DeMMO) is situated in a range of iron-rich lithologies, and fracture fluids here reach concentrations as high as 8.84 mg/liter. Iron cycling is likely an important process, given the high concentrations of iron in fracture fluids and detection of putative iron-cycling taxa via marker gene surveys. However, a previous metagenomic survey detected no iron cycling potential at two DeMMO localities. Here, we revisited the potential for iron cycling at DeMMO using a new metagenomic data set including all DeMMO sites and FeGenie, a new annotation pipeline that is optimized for the detection of iron cycling genes. We annotated functional genes from whole metagenomic assemblies and metagenome-assembled genomes and characterized putative iron cycling pathways and taxa in the context of local geochemical conditions and available metabolic energy estimated from thermodynamic models. We reannotated previous metagenomic data, revealing iron cycling potential that was previously missed. Across both metagenomic data sets, we found that not only is there genetic potential for iron cycling at DeMMO, but also, iron is likely an important source of energy across the system. In response to the dramatic differences we observed between annotation approaches, we recommend the use of optimized pipelines where the detection of iron cycling genes is a major goal. IMPORTANCE We investigated iron cycling potential among microbial communities inhabiting iron-rich fracture fluids to a depth of 1.5 km in the continental crust. A previous study found no iron cycling potential in the communities despite the iron-rich nature of the system. A new tool for detecting iron cycling genes was recently published, which we used on a new data set. We combined this with a number of other approaches to get a holistic view of metabolic strategies across the communities, revealing iron cycling to be an important process here. In addition, we used the tool on the data from the previous study, revealing previously missed iron cycling potential. Iron is common in continental crust; thus, our findings are likely not unique to our study site. Our new view of important metabolic strategies underscores the importance of choosing optimized tools for detecting the potential for metabolisms like iron cycling that may otherwise be missed.

Homogeneous Cytochrome 579 Is an Octamer That Reacts Too Slowly With Soluble Iron to Be the Initial Iron Oxidase in the Respiratory Chain of Leptospirillum ferriphilum

The exact role that cytochrome 579 plays in the aerobic iron respiratory chain of Leptospirillum ferriphilum is unclear. This paper presents genomic, structural, and kinetic data on the cytochrome 579 purified from cell-free extracts of L. ferriphilum cultured on soluble iron. Electrospray mass spectrometry of electrophoretically homogeneous cytochrome 579 yielded two principal peaks at 16,015 and 16,141 Daltons. N-terminal amino acid sequencing of the purified protein yielded data that were used to determine the following: there are seven homologs of cytochrome 579; each homolog possesses the CXXCH heme-binding motif found in c-type cytochromes; each of the seven sequenced strains of L. ferriphilum expresses only two of the seven homologs of the cytochrome; and each homolog contains an N-terminal signal peptide that directs the mature protein to an extra-cytoplasmic location. Static light scattering and macroion mobility measurements on native cytochrome 579 yielded masses of 125 and 135 kDaltons, respectively. The reduced alkaline pyridine hemochromogen spectrum of the purified cytochrome had an alpha absorbance maximum at 567 nm, a property not exhibited by any known heme group. The iron-dependent reduction and oxidation of the octameric cytochrome exhibited positively cooperative kinetic behavior with apparent Hill coefficients of 5.0 and 3.7, respectively, when the purified protein was mixed with mM concentrations of soluble iron. Consequently, the extrapolated rates of reduction at sub-mM iron concentrations were far too slow for cytochrome 579 to be the initial iron oxidase in the aerobic respiratory chain of L. ferriphilum. Rather, these observations support the hypothesis that the acid-stable cytochrome 579 is a periplasmic conduit of electrons from initial iron oxidation in the outer membrane of this Gram-negative bacterium to a terminal oxidase in the plasma membrane.

Dissulfurispira thermophila gen. nov., sp. nov., a thermophilic chemolithoautotroph growing by sulfur disproportionation, and proposal of novel taxa in the phylum Nitrospirota to reclassify the genus Thermodesulfovibrio

Recently, presence of sulfur-disproportionating bacterial species belonging to the phylum Nitrospirota was indicated by an enrichment culture-based study. In the present study, a strain representing that species was isolated and characterized. The strain, strain T55J^T, was isolated from a microbial mat of a hot spring. The cells were motile, and rods or spiral forms with width of 0.32-0.49 μm. The strain grew autotrophically, only by disproportionation of thiosulfate or elemental sulfur. Growth was observed at a temperature range of 25-60°C, with optimum growth at 53-57°C. The pH range for growth was 5.5-9.0, with optimum pH of 7.0-8.0. The complete genome of strain T55J^T is composed of a circular chromosome (2,370,875 bp), with G+C content of 38.7%. Thermodesulfovibrio hydrogeniphilus Hdr5^T showed the highest sequence similarity of the 16S rRNA gene to strain T55J^T, but it was only 88.2%. On the basis of the phylogenetic and physiologic properties, strain T55J^T (= DSM 110365^T=NBRC 114245^T) is proposed as type strain of a novel species in a new genus, Dissulfurispira thermophila gen. nov., sp. nov. To assign the new genus to family and higher taxa, its taxonomic position was assessed by genome-based phylogeny. As a result, it was shown that the novel genus and Thermodesulfovibrio belong to different families. It was also shown that Thermodesulfovibrio should be reclassified at levels from class to family and creation of some novel taxa is required. Based on these results, Thermodesulfovibrionia class. nov., Thermodesulfovibrionales ord. nov., Thermodesulfovibrionaceae fam. nov., and Dissulfurispiraceae fam. nov. are proposed.

Microbial Community Structure Along a Horizontal Oxygen Gradient in a Costa Rican Volcanic Influenced Acid Rock Drainage System

We describe the geochemistry and microbial diversity of a pristine environment that resembles an acid rock drainage (ARD) but it is actually the result of hydrothermal and volcanic influences. We designate this environment, and other comparable sites, as volcanic influenced acid rock drainage (VARD) systems. The metal content and sulfuric acid in this ecosystem stem from the volcanic milieu and not from the product of pyrite oxidation. Based on the analysis of 16S rRNA gene amplicons, we report the microbial community structure in the pristine San Cayetano Costa Rican VARD environment (pH = 2.94-3.06, sulfate ~ 0.87-1.19 g L^-1, iron ~ 35-61 mg L^-1 (waters), and ~ 8-293 g kg^-1 (sediments)). San Cayetano was found to be dominated by microorganisms involved in the geochemical cycling of iron, sulfur, and nitrogen; however, the identity and abundance of the species changed with the oxygen content (0.40-6.06 mg L^-1) along the river course. The hypoxic source of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium. Sulfur-oxidizing bacteria such as Acidithiobacillus or Sulfobacillus are found in smaller proportions with respect to typical ARD. In the oxic downstream, we identified aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferrovum) and heterotrophic bacteria (Burkholderiaceae bacterium, Trichococcus, Acidocella). Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD niches were also observed throughout the entire ecosystem. Overall, our study shows the differences and similarities in the diversity and distribution of the microbial communities between an ARD and a VARD system at the source and along the oxygen gradient that establishes on the course of the river.

Interactions Between Cells of Sulfobacillus thermosulfidooxidans and Leptospirillum ferriphilum During Pyrite Bioleaching

Sulfobacillus and Leptospirillum occur frequently in leaching systems. Here we investigated the effects of cells of L. ferriphilum on biofilm formation and leaching performance by S. thermosulfidooxidans. The effects were caused by the presence of L. ferriphilum or an addition of pyrite leach liquor from L. ferriphilum. Data show that the number of attached S. thermosulfidooxidans on pyrite increases, if the pyrite had been pre-colonized by living biofilms of L. ferriphilum, while it decreases if the pre-colonized biofilms had been inactivated. Coaggregation between S. thermosulfidooxidans and L. ferriphilum occurs during the dual-species biofilm formation, but different effects on bioleaching were noted, if the preculture of L. ferriphilum had been different. If L. ferriphilum had been pre-colonized on a pyrite, significantly negative effect was shown. However, if the two species were simultaneously inoculated into a sterile leaching system, the bioleaching efficiency was better than that of a pure culture of S. thermosulfidooxidans. The effect might be related to a metabolic preference of S. thermosulfidooxidans. If S. thermosulfidooxidans performed leaching in a filtered pyrite leachate from L. ferriphilum, the cells preferred to oxidize RISCs instead of ferrous ion and the number of attached cells decreased compared with the control. This study gives an indication that in a short-term multi-species leaching system the role of S. thermosufidooxidans may be related to the time of its introduction.

Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium

Possibilities for the recovery of non-ferrous and precious metals from Kapan polymetallic mine tailings (Armenia) were studied. The aim of this paper was to study the possibilities of bioleaching of samples of concentrated tailings by the natural microbial consortium of drainage water. The extent of extraction of metals from the samples of concentrated tailings by natural microbial consortium reached 41-55% and 53-73% for copper and zinc, respectively. Metal leaching efficiencies of pure culture Leptospirillum ferrooxidans Teg were higher, namely 47-93% and 73-81% for copper and zinc, respectively. The content of gold in solid phase of tailings increased about 7-16% and 2-9% after bio-oxidation process by L. ferrooxidans Teg and natural microbial consortium, respectively. It was shown that bioleaching of the samples of tailings could be performed using the natural consortium of drainage water. However, to increase the intensity of the recovery of valuable metals, natural consortium of drainage water combined with iron-oxidizing L. ferrooxidans Teg has been proposed.

Soil Microbiome Dynamics During Pyritic Mine Tailing Phytostabilization: Understanding Microbial Bioindicators of Soil Acidification

Challenges to the reclamation of pyritic mine tailings arise from in situ acid generation that severely constrains the growth of natural revegetation. While acid mine drainage (AMD) microbial communities are well-studied under highly acidic conditions, fewer studies document the dynamics of microbial communities that generate acid from pyritic material under less acidic conditions that can allow establishment and support of plant growth. This research characterizes the taxonomic composition dynamics of microbial communities present during a 6-year compost-assisted phytostabilization field study in extremely acidic pyritic mine tailings. A complementary microcosm experiment was performed to identify successional community populations that enable the acidification process across a pH gradient. Taxonomic profiles of the microbial populations in both the field study and microcosms reveal shifts in microbial communities that play pivotal roles in facilitating acidification during the transition between moderately and highly acidic conditions. The potential co-occurrence of organoheterotrophic and lithoautotrophic energy metabolisms during acid generation suggests the importance of both groups in facilitating acidification. Taken together, this research suggests that key microbial populations associated with pH transitions could be used as bioindicators for either sustained future plant growth or for acid generation conditions that inhibit further plant growth.

Adhesion to Mineral Surfaces by Cells of Leptospirillum, Acidithiobacillus and Sulfobacillus from Armenian Sulfide Ores

Bioleaching of metal sulfides is an interfacial process where adhesion and subsequent biofilm formation are considered to be crucial for this process. In this study, adhesion and biofilm formation by several acidophiles (Acidithiobacillus, Leptospirillum and Sulfobacillus) isolated from different biotopes with sulfide ores in Armenia were studied. Results showed that: (1) these bacteria adhere to pyrite surfaces to various extents. A correlation between pyrite biooxidation and adhesion of S. thermosulfidooxidans 6, L. ferriphilum CC, L. ferrooxidans ZC on pyrite surfaces is shown. It is supposed that bioleaching of pyrite by S. thermosulfidooxidans 6, L. ferriphilum CC, L. ferrooxidans ZC occurs by means of indirect leaching: by ferric iron of bacterial origin; (2) cells of At. ferrooxidans 61, L. ferrooxidans ZC and St. thermosulfidooxidans 6 form a monolayer biofilm on pyrite surfaces. The coverage of pyrite surfaces varies among these species. The order of the biofilm coverage is: L. ferrooxidans ZC ≥ At. ferrooxidans 61 > St. thermosulfidooxidans 6; (3) the extracellular polymeric substances (EPS) analysis indicates that the tested strains produce EPS, if grown either on soluble ferrous iron or solid pyrite. EPS are mainly composed of proteins and carbohydrates. Cells excrete higher amounts of capsular EPS than of colloidal EPS. In addition, cells grown on pyrite produce more EPS than ones grown on ferrous iron.

Biological oxidation of iron sulfides

The biological oxidation of minerals and ores, called bioleaching, has been studied for the last decades to solubilize metals and recover them. In particular, iron sulfides are the most studied ores for an optimum extraction of different metals, such as copper or zinc. The use of chemolithotrophic bacteria, as Acidothiobacillus ferrooxidans, to oxidize both iron and sulfur species in aerobic conditions and at acidic pH shows promising results. In the field of heritage preservation, the development of "green" treatments is more and more studied. Waterlogged archeological wood presents an accumulation of iron sulfides within its structure, which, after exposition to oxygen, lead to salt precipitation and acidification and so to the degradation of the wooden artifact. A new extraction method, based on the dissolution of iron sulfides by the use of bacteria could be an alternative to the current chemical extraction methods, as being more respectful and ecological. While A. ferrooxidans is very effective in mines and groundwater, in the field of conservation-restoration of wood, Thiobacillus denitrificans is a better candidate as it grows at neutral pH, which is less aggressive for organic substrates (wood here). Preliminary studies show the efficiency of T. denitrificans for the dissolution of iron sulfides, as the concentration of nitrates used as electron donors decreases while the concentration of sulfates produced increases without degrading the wooden matrix. Long-term behavior should be studied to assess the stability of the artifacts after treatment.

Pan-Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation

Niche adaptation has long been recognized to drive intra-species differentiation and speciation, yet knowledge about its relatedness with hereditary variation of microbial genomes is relatively limited. Using Leptospirillum ferriphilum species as a case study, we present a detailed analysis of genomic features of five recognized strains. Genome-to-genome distance calculation preliminarily determined the roles of spatial distance and environmental heterogeneity that potentially contribute to intra-species variation within L. ferriphilum species at the genome level. Mathematical models were further constructed to extrapolate the expansion of L. ferriphilum genomes (an 'open' pan-genome), indicating the emergence of novel genes with new sequenced genomes. The identification of diverse mobile genetic elements (MGEs) (such as transposases, integrases, and phage-associated genes) revealed the prevalence of horizontal gene transfer events, which is an important evolutionary mechanism that provides avenues for the recruitment of novel functionalities and further for the genetic divergence of microbial genomes. Comprehensive analysis also demonstrated that the genome reduction by gene loss in a broad sense might contribute to the observed diversification. We thus inferred a plausible explanation to address this observation: the community-dependent adaptation that potentially economizes the limiting resources of the entire community. Now that the introduction of new genes is accompanied by a parallel abandonment of some other ones, our results provide snapshots on the biological fitness cost of environmental adaptation within the L. ferriphilum genomes. In short, our genome-wide analyses bridge the relation between genetic variation of L. ferriphilum with its evolutionary adaptation.

Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications

Acidithiobacillus ferrooxidans is a gram-negative chemolithoautotrophic γ-proteobacterium. It typically grows at an external pH of 2 using the oxidation of ferrous ions by oxygen, producing ferric ions and water, while fixing carbon dioxide from the environment. A. ferrooxidans is of great interest for biomining and environmental applications, as it can process mineral ores and alleviate the negative environmental consequences derived from the mining processes. In this study, the first genome-scale metabolic reconstruction of A. ferrooxidans ATCC 23270 was generated (iMC507). A total of 587 metabolic and transport/exchange reactions, 507 genes and 573 metabolites organized in over 42 subsystems were incorporated into the model. Based on a new genetic algorithm approach, that integrates flux balance analysis, chemiosmotic theory, and physiological data, the proton translocation stoichiometry for a number of enzymes and maintenance parameters under aerobic chemolithoautotrophic conditions using three different electron donors were estimated. Furthermore, a detailed electron transfer and carbon flux distributions during chemolithoautotrophic growth using ferrous ion, tetrathionate and thiosulfate were determined and reported. Finally, 134 growth-coupled designs were calculated that enables Extracellular Polysaccharide production. iMC507 serves as a knowledgebase for summarizing and categorizing the information currently available for A. ferrooxidans and enables the understanding and engineering of Acidithiobacillus and similar species from a comprehensive model-driven perspective for biomining applications.

Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile

Leptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod-shaped bacterium, isolated from an industrial bioleaching operation in northern Chile, where chalcocite is the major copper mineral and copper hydroxychloride atacamite is present in variable proportions in the ore. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of chloride, sulfate and metals. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 2,475,669 bp draft genome is arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834 protein coding genes were predicted from its annotation; 55 % of these were assigned a putative function. Release of the genome sequence of this strain will provide further understanding of the mechanisms used by acidophilic bacteria to endure high osmotic stress and high chloride levels and of the role of chloride-tolerant iron-oxidizers in industrial bioleaching operations.

Ecotoxic heavy metals transformation by bacteria and fungi in aquatic ecosystem

Water is the most important and vital molecule of our planet and covers 75% of earth surface. But it is getting polluted due to high industrial growth. The heavy metals produced by industrial activities are recurrently added to it and considered as dangerous pollutants. Increasing concentration of toxic heavy metals (Pb(2+), Cd(2+), Hg(2+), Ni(2+)) in water is a severe threat for human. Heavy metal contaminated water is highly carcinogenic and poisonous at even relatively low concentrations. When they discharged in water bodies, they dissolve in the water and are distributed in the food chain. Bacteria and fungi are efficient microbes that frequently transform heavy metals and remove toxicity. The application of bacteria and fungi may offer cost benefit in water treatment plants for heavy metal transformation and directly related to public health and environmental safety issues. The heavy metals transformation rate in water is also dependent on the enzymatic capability of microorganisms. By transforming toxic heavy metals microbes sustain aquatic and terrestrial life. Therefore the application of microbiological biomass for heavy metal transformation and removal from aquatic ecosystem is highly significant and striking. This paper reviews the microbial transformation of heavy metal, microbe metal interaction and different approaches for microbial heavy metal remediation from water bodies.

Manipulation of pyrite colonization and leaching by iron-oxidizing Acidithiobacillus species

In this study, the process of pyrite colonization and leaching by three iron-oxidizing Acidithiobacillus species was investigated by fluorescence microscopy, bacterial attachment, and leaching assays. Within the first 4-5 days, only the biofilm subpopulation was responsible for pyrite dissolution. Pyrite-grown cells, in contrast to iron-grown cells, were able to oxidize iron(II) ions or pyrite after 24 h iron starvation and incubation with 1 mM H₂O₂, indicating that these cells were adapted to the presence of enhanced levels of reactive oxygen species (ROS), which are generated on metal sulfide surfaces. Acidithiobacillus ferrivorans SS3 and Acidithiobacillus ferrooxidans R1 showed enhanced pyrite colonization and biofilm formation compared to A. ferrooxidans (T). A broad range of factors influencing the biofilm formation on pyrite were also identified, some of them were strain-specific. Cultivation at non-optimum growth temperatures or increased ionic strength led to a decreased colonization of pyrite. The presence of iron(III) ions increased pyrite colonization, especially when pyrite-grown cells were used, while the addition of 20 mM copper(II) ions resulted in reduced biofilm formation on pyrite. This observation correlated with a different extracellular polymeric substance (EPS) composition of copper-exposed cells. Interestingly, the addition of 1 mM sodium glucuronate in combination with iron(III) ions led to a 5-fold and 7-fold increased cell attachment after 1 and 8 days of incubation, respectively, in A. ferrooxidans (T). In addition, sodium glucuronate addition enhanced pyrite dissolution by 25%.

Draft Genome Sequence of the Iron-Oxidizing Acidophile Leptospirillum ferriphilum Type Strain DSM 14647

The genomic features of the Leptospirillum ferriphilum type strain DSM 14647 are described here. An analysis of the predicted genes enriches our knowledge of the molecular basis of iron oxidation, improves our understanding of its role in industrial bioleaching, and suggests how it is adapted to live at extremely low pH.

A concise review of nanoscopic aspects of bioleaching bacteria-mineral interactions

Bioleaching is a technology for the recovery of metals from minerals by means of microorganisms, which accelerate the oxidative dissolution of the mineral by regenerating ferric ions. Bioleaching processes take place at the interface of bacteria, sulfide mineral and leaching solution. The fundamental forces between a bioleaching bacterium and mineral surface are central to understanding the intricacies of interfacial phenomena, such as bacterial adhesion or detachment from minerals and the mineral dissolution. This review focuses on the current state of knowledge in the colloidal aspect of bacteria-mineral interactions, particularly for bioleaching bacteria. Special consideration is given to the microscopic structure of bacterial cells and the atomic force microscopy technique used in the quantification of fundamental interaction forces at nanoscale.

Bacterial recovery and recycling of tellurium from tellurium-containing compounds by Pseudoalteromonas sp. EPR3

AIMS

Tellurium-based devices, such as photovoltaic (PV) modules and thermoelectric generators, are expected to play an increasing role in renewable energy technologies. Tellurium, however, is one of the scarcest elements in the earth's crust, and current production and recycling methods are inefficient and use toxic chemicals. This study demonstrates an alternative, bacterially mediated tellurium recovery process.

METHODS AND RESULTS

We show that the hydrothermal vent microbe Pseudoalteromonas sp. strain EPR3 can convert tellurium from a wide variety of compounds, industrial sources and devices into metallic tellurium and a gaseous tellurium species. These compounds include metallic tellurium (Te(0)), tellurite (TeO3(2-)), copper autoclave slime, tellurium dioxide (TeO2), tellurium-based PV material (cadmium telluride, CdTe) and tellurium-based thermoelectric material (bismuth telluride, Bi2Te3). Experimentally, this was achieved by incubating these tellurium sources with the EPR3 in both solid and liquid media.

CONCLUSIONS

Despite the fact that many of these tellurium compounds are considered insoluble in aqueous solution, they can nonetheless be transformed by EPR3, suggesting the existence of a steady state soluble tellurium concentration during tellurium transformation.

SIGNIFICANCE AND IMPACT OF THE STUDY

These experiments provide insights into the processes of tellurium precipitation and volatilization by bacteria, and their implications on tellurium production and recycling.

Bioleaching of a low-grade nickel-copper sulfide by mixture of four thermophiles

This study investigated thermophilic bioleaching of a low grade nickel-copper sulfide using mixture of four acidophilic thermophiles. Effects of 0.2g/L l-cysteine on the bioleaching process were further evaluated. It aimed at offering new alternatives for enhancing metal recoveries from nickel-copper sulfide. Results showed a recovery of 80.4% nickel and 68.2% copper in 16-day bioleaching without l-cysteine; while 83.7% nickel and 81.4% copper were recovered in the presence of l-cysteine. Moreover, nickel recovery was always higher than copper recovery. l-Cysteine was found contributing to lower pH value, faster microbial growth, higher Oxidation-Reduction Potential (ORP), higher zeta potential and absorbing on the sulfide surfaces through amino, carboxyl and sulfhydryl groups. X-ray Diffraction (XRD) patterns of leached residues showed generation of S, jarosite and ammoniojarosite. Denaturing Gradient Gel Electrophoresis (DGGE) results revealed that l-cysteine could have variant impacts on different microorganisms and changed the microbial community composition dramatically during nickel-copper sulfide bioleaching.

Geomicrobiology of La Zarza-Perrunal acid mine effluent (Iberian Pyritic Belt, Spain)

Effluent from La Zarza-Perrunal, a mine on the Iberian Pyrite Belt, was chosen to be geomicrobiologically characterized along a 1,200-m stream length. The pH at the origin was 3.1, which decreased to 1.9 at the final downstream sampling site. The total iron concentration showed variations along the effluent, resulting from (i) significant hydrolysis and precipitation of Fe(III) (especially along the first reach of the stream) and (ii) concentration induced by evaporation (mostly in the last reach). A dramatic increase in iron oxidation was observed along the course of the effluent [from Fe(III)/Fe(total) = 0.11 in the origin to Fe(III)/Fe(total) = 0.99 at the last sampling station]. A change in the O(2) content along the effluent, from nearly anoxic at the origin to saturation with oxygen at the last sampling site, was also observed. Prokaryotic and eukaryotic diversity throughout the effluent was determined by microscopy and 16S rRNA gene cloning and sequencing. Sulfate-reducing bacteria (Desulfosporosinus and Syntrophobacter) were detected only near the origin. Some iron-reducing bacteria (Acidiphilium, Acidobacterium, and Acidosphaera) were found throughout the river. Iron-oxidizing microorganisms (Leptospirillum spp., Acidithiobacillus ferrooxidans, and Thermoplasmata) were increasingly detected downstream. Changes in eukaryotic diversity were also remarkable. Algae, especially Chlorella, were present at the origin, forming continuous, green, macroscopic biofilms, subsequently replaced further downstream by sporadic Zygnematales filaments. Taking into consideration the characteristics of this acidic extreme environment and the physiological properties and spatial distribution of the identified microorganisms, a geomicrobiological model of this ecosystem is advanced.

Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways

Autotrophic acidophilic iron- and sulfur-oxidizing bacteria of the genus Acidithiobacillus constitute a heterogeneous taxon encompassing a high degree of diversity at the phylogenetic and genetic levels, though currently only two species are recognized (Acidithiobacillus ferrooxidans and Acidithiobacillus ferrivorans). One of the major functional disparities concerns the biochemical mechanisms of iron and sulfur oxidation, with discrepancies reported in the literature concerning the genes and proteins involved in these processes. These include two types of high-potential iron–sulfur proteins (HiPIPs): (i) Iro, which has been described as the iron oxidase; and (ii) Hip, which has been proposed to be involved in the electron transfer between sulfur compounds and oxygen. In addition, two rusticyanins have been described: (i) rusticyanin A, encoded by the rusA gene and belonging to the well-characterized rus operon, which plays a central role in the iron respiratory chain; and (ii) rusticyanin B, a protein to which no function has yet been ascribed. Data from a multilocus sequence analysis of 21 strains of Fe(II)-oxidizing acidithiobacilli obtained from public and private collections using five phylogenetic markers showed that these strains could be divided into four monophyletic groups. These divisions correlated not only with levels of genomic DNA hybridization and phenotypic differences among the strains, but also with the types of rusticyanin and HiPIPs that they harbour. Taken together, the data indicate that Fe(II)-oxidizing acidithiobacilli comprise at least four distinct taxa, all of which are able to oxidize both ferrous iron and sulfur, and suggest that different iron oxidation pathways have evolved in these closely related bacteria.

GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage

Acid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, gene overlapping, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 2.0 were detected in the AMD microbial communities, including carbon fixation, carbon degradation, methane generation, nitrogen fixation, nitrification, denitrification, ammonification, nitrogen reduction, sulfur metabolism, metal resistance, and organic contaminant degradation, which suggested that the functional gene diversity was higher than was previously thought. Mantel test results indicated that AMD microbial communities are shaped largely by surrounding environmental factors (e.g., S, Mg, and Cu). Functional genes (e.g., narG and norB) and several key functional processes (e.g., methane generation, ammonification, denitrification, sulfite reduction, and organic contaminant degradation) were significantly (P < 0.10) correlated with environmental variables. This study presents an overview of functional gene diversity and the structure of AMD microbial communities and also provides insights into our understanding of metabolic potential in AMD ecosystems.

Partial Removal of Lipopolysaccharide from Thiobacillus ferrooxidans Affects Its Adhesion to Solids

Conditions for the partial removal of lipopolysaccharide (LPS) from Thiobacillus ferrooxidans are described. Raising the pH of the solution containing the cells from pH 1.5 to pH 6.8 to 8.0 releases about 50% of the LPS without cell lysis. The release of LPS begins at pH 3.5, and it was not affected by EDTA concentration. Partial removal of LPS exposed higher amounts of a 40-kDa outer membrane protein in the bacteria, as detected by a dot immunoassay employing an antiserum against the T. ferrooxidans surface protein. This higher protein exposure and the reduced LPS content increased the hydrophobicity of the cell surface, as determined by an increased adhesion (50%) to hydrophobic sulfur prills and C-dodecanoic acid binding (2.5-fold) compared with control cells. In addition, adhesion of radioactively labeled microorganisms to a sulfide mineral was inhibited (40%) in the presence of previously added LPS. Our results suggest that not only LPS but also surface proteins probably play important roles in T. ferrooxidans adhesion to solid surfaces.

Sulfur chemistry in bacterial leaching of pyrite

In the case of pyrite bioleaching by Leptospirillum ferrooxidans, an organism without sulfur-oxidizing capacity, besides the production of tetra- and pentathionate, a considerable accumulation of elemental sulfur occurred. A similar result was obtained for chemical oxidation assays with acidic, sterile iron(III) ion-containing solutions. In the case of Thiobacillus ferrooxidans, only slight amounts of elemental sulfur were detectable because of the organism's capacity to oxidize sulfur compounds. In the course of oxidative, chemical pyrite degradation under alkaline conditions, the accumulation of tetrathionate, trithionate, and thiosulfate occurred. The data indicate that thiosulfate, trithionate, tetrathionate, and disulfane-monosulfonic acid are key intermediate sulfur compounds in oxidative pyrite degradation. A novel (cyclic) leaching mechanism is proposed which basically is indirect.

Microbial diversity in uranium mine waste heaps

Two different uranium mine waste heaps near Ronneburg, Thuringia, Germany, which contain the remains of the activity of the former uranium-mining Soviet-East German company Wismut AG, were analyzed for the occurrence of lithotrophic and chemoorganotropic leach bacteria. A total of 162 ore samples were taken up to a depth of 5 m. Cell counts of ferrous iron-, sulfur-, sulfur compound-, ammonia-, and nitrite-oxidizing bacteria were determined quantitatively by the most-probable-number technique. Sulfate-, nitrate-, ferric iron-, and manganese-reducing bacteria were also detected. In addition, the metabolic activity of sulfur- and iron-oxidizing bacteria was measured by microcalorimetry. Generally, all microorganisms mentioned above were detectable in the heaps. Aerobic and anaerobic microorganisms thrived up to a depth of 1.5 to 2 m. Up to 99% of Thiobacillus ferrooxidans cells, the dominant leaching bacteria, occurred to this depth. Their numbers correlated with the microbial activity measurements. Samples below 1.5 to 2 m exhibited reduced oxygen concentrations and reduced cell counts for all microorganisms.

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.

Microbial communities in acid mine drainage

The dissolution of sulfide minerals such as pyrite (FeS2), arsenopyrite (FeAsS), chalcopyrite (CuFeS2), sphalerite (ZnS), and marcasite (FeS2) yields hot, sulfuric acid-rich solutions that contain high concentrations of toxic metals. In locations where access of oxidants to sulfide mineral surfaces is increased by mining, the resulting acid mine drainage (AMD) may contaminate surrounding ecosystems. Communities of autotrophic and heterotrophic archaea and bacteria catalyze iron and sulfur oxidation, thus may ultimately determine the rate of release of metals and sulfur to the environment. AMD communities contain fewer prokaryotic lineages than many other environments. However, it is notable that at least two archaeal and eight bacterial divisions have representatives able to thrive under the extreme conditions typical of AMD. AMD communities are characterized by a very limited number of distinct species, probably due to the small number of metabolically beneficial reactions available. The metabolisms that underpin these communities include organoheterotrophy and autotrophic iron and sulfur oxidation. Other metabolic activity is based on anaerobic sulfur oxidation and ferric iron reduction. Evidence for physiological synergy in iron, sulfur, and carbon flow in these communities is reviewed. The microbial and geochemical simplicity of these systems makes them ideal targets for quantitative, genomic-based analyses of microbial ecology and evolution and community function.

Leptospirillum ferrooxidans based Fe2+ sensor

A novel electrochemical biosensor integrating the strictly autotrophic bacterial strain Leptospirillum ferrooxidans as a recognition element and a Clark type oxygen probe as a transducer was designed, metrologically and analytically characterized and applied for the specific Fe(2+) determination. The bacterial Fe(2+) oxidation involves O(2) consumption, thus the quantification was performed registering the decrease of the oxygen reduction current. The limit of detection was found to be 2.4 micromol L(-1) and the sensitivity of the determinations-3.94 nAL micromol(-1). The response time of the biosensor is 18s for Fe(2+) concentrations of 10(-5) to 10(-4) mol L(-1). The biosensor was applied as well for the indirect determination of Fe(2+) oxidizing species such as Cr(2)O(7)(2-), reaching a sensitivity of 2.47 nAL micromol(-1). The transducer characteristics were evaluated and optimized to obtain short response time and high sensitivity. The analytical performances of the biosensor subject of the present work were found to be similar to that of the At. ferrooxidans based one developed by the authors earlier, avoiding however the sulfur compounds interference, because of the substrate specificity of the applied bacterial strain.

Interfacial activity and leaching patterns of Leptospirillum ferrooxidans on pyrite

The leaching ability of Leptospirillum ferrooxidans goes beyond the mere oxidation of Fe(2+) to Fe(3+). Addition of these bacteria to pyrite triggers interfacial phenomena that lead to bacterial attachment and local forms of corrosion (surface pitting). As the leaching process proceeds, bacterial cells undergo changes, characterized by the release of extracellular polymeric substances (EPS) and the uptake and storage of electro-dense nanoparticles. The latter are embedded in an exopolymeric capsule, which coats the bacterial surface leading to distinctive biomineralized assemblages. High-resolution scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analyses, quantitative energy-dispersive X-ray measurements and electron diffraction established that the embedded electron-dense nanoparticles comprise pyrite with a well-defined stoichiometry. Addition of Fe(3+) alone did not induce any form of local corrosion on pyrite, which indicates that the reactions taking place between the attached bacteria and the underlying pyrite surface are responsible for the leaching patterns observed in this study. The observed corrosion process resembles that of 'electrochemical machining', because it uses a corrosion promoter, namely the locally concentrated Fe(3+) in the biofilm environment, formed by the attached cells.