Potential application of a knowledgebase of iron metabolism of Acidithiobacillus ferrooxidans as an alternative platform

BACKGROUND: Acidithiobacillus ferrooxidans is a facultative anaerobe that depends on ferrous ion oxidation as well as reduced sulfur oxidation to obtain energy and is widely applied in metallurgy, environmental protection, and soil remediation. With the accumulation of experimental data, metabolic mechanisms, kinetic models, and several databases have been established. However, scattered data are not conducive to understanding A. ferrooxidans that necessitates updated information informed by systems biology. RESULTS: Here, we constructed a knowledgebase of iron metabolism of A. ferrooxidans (KIMAf) system by integrating public databases and reviewing the literature, including the database of bioleaching substrates (DBS), the database of bioleaching metallic ion-related proteins (MIRP), the A. ferrooxidans bioinformation database (Af-info), and the database for dynamics model of bioleaching (DDMB). The DBS and MIRP incorporate common bioleaching substrates and metal ion-related proteins. Af-info and DDMB integrate nucleotide, gene, protein, and kinetic model information. Statistical analysis was performed to elucidate the distribution of isolated A. ferrooxidans strains, evolutionary and metabolic advances, and the development of bioleaching models. CONCLUSIONS: This comprehensive system provides researchers with a platform of available iron metabolism-related resources of A. ferrooxidans and facilitates its application.

Molecular ecological network reveals the response of metallurgical microorganisms to energy substrates / 生物工程学报

By analyzing the shift of microbial communities under different iron/sulfur ratios, the response of metallurgical microorganisms to energy substrates was investigated based on molecular ecological networks. High-throughput sequencing of microbial samples from different domesticated batches was conducted to analyze the changes in community composition, alpha and beta diversity. Based on the molecular ecological network, the interactions between microorganisms under different iron/sulfur ratios were explored. Keystones were identified to analyze the community response to energy substrates. In the process of domestication based on different energy substrates, the dominant species in the in iron-rich and sulfur-less community were Acidithiobacillus ferrooxidans and A. ferriphilus. A. thiooxidans accounted for up to 90% in the sulfur-rich and iron-less community after 3 domesticating batches. The results of alpha and beta diversity analysis show that the domestication process of sulfur-rich and iron-less substrates reduced the diversity of microbial communities. Molecular ecological network analysis shows that the keystones were all rare species with low abundance. During the domestication by sulfur-rich and iron-less energy substrates, the bacterial species had a closer symbiotic relationship and the community was more stable. Through this domestication experiment, the impact of different energy substrates on microbial aggregation was clarified. Domesticating metallurgical microorganisms by using sulfur-rich and iron-less energy substrates made the microbial colonies to be more stable, which was conducive to the oxidation of iron and sulfur, promoting the dissolution of sulfide minerals. Our findings provide a reference for the directional domestication of metallurgical microorganisms.

Bioleaching of realgar nanoparticles using the extremophilic bacterium Acidithiobacillus ferrooxidans DLC-5

BACKGROUND: This paper presents micro- and nano-fabrication techniques for leachable realgar using the extremophilic bacterium Acidithiobacillus ferrooxidans (A. ferrooxidans) DLC-5. RESULTS: Realgar nanoparticles of size ranging from 120 nm to 200 nm were successfully prepared using the highenergy ball mill instrument. A. ferrooxidans DLC-5 was then used to bioleach the particles. The arsenic concentration in the bioleaching system was found to be increased significantly when compared with that in the sterile control. Furthermore, in the comparison with the bioleaching of raw realgar, nanoparticles could achieve the same effect with only one fifth of the consumption. CONCLUSION: Emphasis was placed on improving the dissolvability of arsenic because of the great potential of leachable realgar drug delivery in both laboratory and industrial settings

Study on the jarosite mediated by bioleaching of pyrrhotite using Acidthiobacillus ferrooxidans / Estudo sobre a jarosita mediada pela biolixiviação da pirrotita usando Acidithiobacillus ferrooxidans

Precipitation of jarosite is a very important phenomenon that is observed in the bioleaching of pyrrhotite by Acidthiobacillus ferrooxidans (A. ferrooxidans). Jarosite is a major secondary mineral formed in acid supergene environment by oxidation of metal sulphide. The formation of jarosite could decrease leached percentage. The Eh-pH diagram of FeS1.12-H2O showed that the thermodynamic parameters of the jarosite were exists steadily on Eh=360 ～ 800, pH=2.8 ～ 5, and the results of pH condition test is consonant with the conclusions of thermodynamic analysis. By means of XRD and SEM, it could indicate that full propagation of A. ferrooxidans in the solution is beneficial to the formation of jarosite and jarosite mediated by bacterial has a better crystalline form than that synthesized by chemical method. This study indicates that pH value and ferrous/ferric iron concentration are key factors affecting the formation of jarosite. Leached percentage is higher when frequency was set more than 2.0. It is crucial to minimize jarosite formation in order to increase factory's efficiency.

A precipitação de jarosite é um fenômeno muito importante que é observado na biolixiviação da pirrotita por Acidithiobacillus ferrooxidans (A. ferrooxidans). A jarosita é um mineral secundário principal formado no ambiente supergênico ácido pela oxidação do sulfureto do metal. A formação de jarosite pode diminuir a porcentagem de lixiviação. O diagrama de Eh-pH de FeS1.12-H2O mostrou que os parâmetros termodinâmicos da jarosite estavam firmemente presentes em Eh = 360~800, pH = 2.8~5, e os resultados do teste de condição de pH estão em consonância com as conclusões da análise termodinâmica. Por meio de XRD e SEM, pode ser indicado que a propagação completa de A. ferrooxidans na solução é benéfica para a formação de jarosite e jarosite mediada por bactérias tem uma forma cristalina melhor do que a sintetizada por método químico. Este estudo indica que o valor do pH e a concentração de ferro ferroso/férrico são fatores chave que afetam a formação de jarosite. A porcentagem de lixiviação é maior quando a freqüência foi ajustada a mais de 2,0. É crucial para minimizar a formação de jarosite, a fim de aumentar a eficiência da fábrica.

Arsenic tolerance and bioleaching from realgar based on response surface methodology by Acidithiobacillus ferrooxidans isolated from Wudalianchi volcanic lake, northeast China

Background: Traditional methods of obtaining arsenic have disadvantages such as high cost and high energy consumption. Realgar is one of the most abundant arsenic sulphide minerals and usually treated as waste in industry. The aim of the present study was to screen an arsenic tolerant bacterium used for bioleaching arsenic from realgar. Results: An acidophilic iron-oxidizing bacterium BYQ-12 was isolated from Wudalianchi volcanic lake in northeast China. BYQ-12 was a motile, rod-shaped gram-negative bacterium with an optimum growth at 30°C and pH 2.5. 16S rDNA phylogeny showed that BYQ-12 was a new strain of Acidithiobacillus ferrooxidans. The inhibitory concentrations (ICs) of arsenite and arsenate were 32 and 64 mM, respectively. A significant second-order model was established using a Box­Behnken design of response surface methodology (BBD-RSM) and it estimated that a maximum arsenic bioleaching rate (73.97%) could be obtained when the pulp concentration, pH and initial ferrous ion concentration were set at optimized values of 0.95% w/v, 1.74 and 3.68 g/L, respectively. SEM, EDS and XRD analyses also revealed that there was direct bioleaching besides indirect electrochemical leaching in the arsenic bioleaching system. Conclusion: From this work we were successful in isolating an acidophilic, arsenic tolerant ferrous iron-oxidizing bacterium. The BBD-RSM analysis showed that maximum arsenic bioleaching rate obtained under optimum conditions, and the most effective factor for arsenic leaching was initial ferrous ion concentration. These revealed that BYQ-12 could be used for bioleaching of arsenic from arsenical minerals.

Interaction of Acidithiobacillus ferrooxidans, Rhizobium phaseoli and Rhodotorula sp. in bioleaching process based on Lotka-Volterra model

Background: Nowadays, leaching-ore bacteria, especially Acidithiobacillus ferrooxidans is widely used to retrieve heavy metals, many researches reflected that extra adding microorganism could promote bioleaching efficiency by different mechanisms, but few of them discussed the interaction between microorganisms and based on growth model. This study aimed to provide theoretical support for the collaborative bioleaching of multiple microorganisms by using the Lotka-Volterra (L-V) model. Results: This study investigated the interaction of Acidithiobacillus ferrooxidans, Rhizobium phaseoli,and Rhodotorula sp. Results showed that the individual growth of the three microorganisms fit the logistic curves. The environmental capacities of A. ferrooxidans, R. phaseoli, and Rhodotorula sp. were 1.88 x 109, 3.26 x 108, and 2.66 x 108 cells/mL, respectively. Co-bioleaching showed mutualism between A. ferrooxidans and R. phaseoli with mutualism coefficients of a =1.19and /3 = 0.31, respectively. The relationship between A. ferrooxidans and Rhodotorula sp. could be considered as commensalism. The commensalism coefficient y of the effect of Rhodotorula sp. on A. ferrooxidans was 2.45. The concentrations of A. ferrooxidans and R. phaseoli were 3.59 x 109 and 1.44 x 109 cells/mL in group E, respectively, as predicted by the model. The concentrations of A. ferrooxidans and Rhodotorula sp. were 2.38 x 109 and 2.66 x 108 cells/mL, respectively. The experimental peak values of the concentrations in microorganism groups E and F were detected on different days, but were quite close to the predicted values. Conclusion: The relationship among microorganisms during leaching could be described appropriately by Lotka-Volterra model between the initial and peak values. The relationship of A. ferrooxidans and R. phaseoli could be considered as mutualism, whereas, the relationship of A. ferrooxidans and R. phaseoli could be considered as commensalism.

Heavy Metal Resistance Strategies of Acidophilic Bacteria and Their Acquisition: Importance for Biomining and Bioremediation

Microbial solubilizing of metals in acid environments is successfully used in industrial bioleaching of ores or biomining to extract metals such as copper, gold, uranium and others. This is done mainly by acidophilic and other microorganisms that mobilize metals and generate acid mine drainage or AMD, causing serious environmental problems. However, bioremediation or removal of the toxic metals from contaminated soils can be achieved by using the specific properties of the acidophilic microorganisms interacting with these elements. These bacteria resist high levels of metals by using a few "canonical" systems such as active efflux or trapping of the metal ions by metal chaperones. Nonetheless, gene duplications, the presence of genomic islands, the existence of additional mechanisms such as passive instruments for pH and cation homeostasis in acidophiles and an inorganic polyphosphate-driven metal resistance mechanism have also been proposed. Horizontal gene transfer in environmental microorganisms present in natural ecosystems is considered to be an important mechanism in their adaptive evolution. This process is carried out by different mobile genetic elements, including genomic islands (GI), which increase the adaptability and versatility of the microorganism. This mini-review also describes the possible role of GIs in metal resistance of some environmental microorganisms of importance in biomining and bioremediation of metal polluted environments such as Thiomonas arsenitoxydans, a moderate acidophilic microorganism, Acidithiobacillus caldus and Acidithiobacillus ferrooxidans strains ATCC 23270 and ATCC 53993, all extreme acidophiles able to tolerate exceptionally high levels of heavy metals. Some of these bacteria contain variable numbers of GIs, most of which code for high numbers of genes related to metal resistance. In some cases there is an apparent correlation between the number of metal resistance genes and the metal tolerance of each of these microorganisms. It is expected that a detailed knowledge of the mechanisms that these environmental microorganisms use to adapt to their harsh niche will help to improve biomining and metal bioremediation in industrial processes.

Biooxidación de concentrados de arsenopirita por Acidithiobacillus ferrooxidans en erlenmeyer agitados / Biooxidation of arsenopyrite concentrates by Acidithiobacillus ferrooxidans in shake flasks

Se evaluó el proceso de biooxidación de concentrados de arsenopirita por A. ferrooxidans ATCC 23270, previa adaptación de los microorganismos al mineral y dos tamaños de partícula, pasante malla Tyler 200 (~75μm) y 325 (~45μm). También, se determinó el grado de concentración del mineral mediante DRX y MOLPP/LR, bajo norma ASTM D 2799 de 2009. Los microorganismos fueron adaptados mediante disminución gradual, en etapas sucesivas, de sulfato ferroso y posterior aumento en el contenido de arsenopirita. Finalmente, se llevó a cabo el proceso de biooxidación del mineral sin adición de Fe2+. Después de treinta días de proceso, la disolución de arsénico para la malla Tyler 200 fue de 7550 mgL-1 (18,7%) y para la malla Tyler 325 fue de 2850 mgL-1 (7,1%). Por otra parte, la curva de crecimiento bacteriano mostró que entre los días 6 y 21 de proceso la población bacteriana promedio fue de 1,70x108 cel.mL-1 y de 8,00x107 cel.mL-1 para las mallas Tyler 200 y 325, respectivamente.Por lo tanto, el tamaño de partícula jugó un papel fundamental en la cinética de adaptación de los microorganismos, sugiriendo que a menor tamaño del sustrato empleado mayor dificultad se le presenta al microorganismo para oxidar el mineral.

Arsenopyrite biooxidation process was evaluated with A. ferrooxidans ATCC 23270. The microorganisms were previously adapted to mineral and two different Tyler mesh sizes, 200 (~75μm) and 325 (~45μm). Also, the mineral concentration was made by DRX and MOLPP/LR under ASTM D 2799. The microorganisms were adapted through gradual decreasing of ferrous sulphate in successive state and subsequent arsenopyrite concentration increase. Finally, biooxidation process was carried out without Fe2+. After thirty days of process, Arsenic bioleaching was 7550 mgL-1(18,7%) and 2850 mgL-1 (7,1%) for the 200 and 325 Tyler meshes, respectively.On the other hand, bacterial growth curve showed, between 6 and 21 days of process that the average bacterial population was 1,70x108 cel.mL-1 y de 8,00x107 cel.mL-1 for 200 and 325 Tyler mesh respectively. For this reason, the particle size played an important role in the adaption kinetics of microorganism. The results showed that the microorganism oxide the larger particle size of the mineral easier.

Separation of magnetic bacteria by using a magnetic separator / 生物工程学报

A magnetic separator was used to separate magnetic bacteria based on their magnetotactic characteristics. Acidithiobacillus ferrooxidans, a bacterium that could synthesize intra-cellular nanometer magnetic particles, was investigated as an example. Strong magnetic and weak magnetic cells were separated and collected. On average, the number of the magnetic particles present in the strong magnetic cells is more than that of the weak magnetic cells. Moreover, semisolid-plate magnetophoresis showed that the magnetotaxis of strong magnetic cells was stronger than the weak magnetic cells. These results suggest that the magnetic separator can be used to isolate the magnetic bacteria, which will facilitate the research of magnetic bacteria.

Response of genes for synthesizing the magnetic of Acidithiobacillus ferrooxidans to different concentration of Fe2+ stress / 生物工程学报

Acidithiobacillus ferrooxidans is able to synthesize intra-cellular electron-dense magnetite, which formed by BCM method in Acidithiobacillus ferrooxidans. The whole genome of the type strain Acidithiobacillus ferrooxidans ATCC 23270 was analyzed by bioinformatics and some homolog genes of functional ones in magnetotactic bacteria were available. This study analyzed the different concentration of Fe2+ stress response of mpsA, magA, thy and mamB gene by using real-time PCR analysis. Temporal genes expression profiles were examined in cells subjected to different concentration of FeSO4 x 7H2O stress, they reached to high expression under 150-200 mmol/L FeSO4 x 7H2O stress. With this new method study, it is possible that we could do deeper research to generate a comprehensive description of the mechanism that how Acidithiobacillus ferrooxidans synthesize the magnetic particles.

Gene function and microbial community structure in sulfide minerals bioleaching system based on microarray analysis / 生物工程学报

Biohydrometallergy technology received more and more attention because of its simple process, low cost and kind to environment, especially in dealing with low-grade and complex minerals. However, it is difficult to optimize microorganism species and process parameters in bioleaching procedure because of the lack of suitable bacteria and quantitative analysis methods at micro-level for bioleaching system. This has resulted in the low efficiency and poor yield of the target metal in bioleaching. With the development of microarray and bacteria conservation technology, solutions to the above problems were being found. This article summarizes the latest findings on genetic elucidation and the community structure of microorganisms in sulfide minerals bioleaching system, in the aim of providing a better understanding on the significance of cross-field technology of biohydrometallergy and genomics.