A stoichiometric model of Acidithiobacillus ferrooxidans ATCC 23270 for metabolic flux analysis

A stoichiometric model of Acidithiobacillus ferrooxidans based on the sequenced genome from strain ATCC 23270 is derived and parameterized using genome/pathway databases. The model describes the main aspects of catabolism and anabolism. By the construction and utilization of the mathematical determination of the network, metabolic flux analysis is performed for such a bacterium for the first time and results are successfully verified by comparison to literature values. This first metabolic model of A. ferrooxidans is able to simulate the main aspects of metabolism and will be useful for further investigation and improvement of bioleaching procedures. Biotechnol. Bioeng. 2009;102: 1448–1459. © 2008 Wiley Periodicals, Inc.     

A direct observation of bacterial coverage and biofilm formation by Acidithiobacillus ferrooxidans on chalcopyrite and pyrite surfaces

To obtain a fundamental understanding of the population behaviour of Acidithiobacillus ferrooxidans at chalcopyrite and pyrite surfaces, the early stage attachment behaviour and biofilm formation by this bacterium on chalcopyrite (CuFeS₂) and pyrite (FeS₂) were studied by optical microscopy, Raman spectroscopy, time-of-flight secondary ion mass spectrometry (ToF-SIMS) and electron backscatter diffraction (EBSD). The results indicate there was no significant difference in selectivity of bacterial attachment between chalcopyrite and pyrite. However, the result of ToF-SIMS analysis suggests that the surface of the pyrite was covered more extensively by biofilm than that of the chalcopyrite, which may indicate more extracellular polymeric substances (EPS) formation by bacterial cells growing on pyrite. EBSD and optical image analysis indicated that selectivity of bacterial attachment to chalcopyrite was not significantly affected by crystal orientation. The results also suggest that the bacterial population in defective areas of chalcopyrite was significantly higher than on the polished surfaces.     

铜蓝精矿的生物浸出

采用两种嗜酸硫杆菌(嗜酸氧化亚铁硫杆菌和喜温硫杆菌)对铜蓝进行生物浸出,实验在有或没有4 g/L硫酸亚铁pH 2．0、150转/分、35℃的三角瓶中进行。实验结果表明:用两种菌混合浸出的铜几乎等于嗜酸氧化亚铁硫杆菌单独浸出的铜;另外,亚铁的加入能提高铜的浸出。     

嗜酸氧化亚铁硫杆菌生长动力学

在确定二价铁离子为A.f生长过程中惟一限制性底物条件下,通过考察初始亚铁离子浓度、初始pH值两种影响亚铁离子氧化代谢的主要因素来研究细菌的生长特性,得到以限制性底物亚铁离子浓度为表征的细菌生长曲线。利用基于Monod方程建立的细菌生长动力学方程模型,采用Matlab软件中的Gauss-Newton算法确定了在不同条件下细菌生长动力学参数,包括最大比生长速率μm、Monod常数K及Ro,推导出了不同条件下A.f对数期以底物Fe(Ⅱ)浓度为表征的生长动力学方程。     

Cytochromes c of Acidithiobacillus ferrooxidans

The chemolithoautotrophic Gram-negative bacterium Acidithiobacillus ferrooxidans is versatile and can grow on a number of electron donors and acceptors. In the A. ferrooxidans ATCC 23270 genome, computer analysis identified 11 genes encoding putative cytochromes c. At least eight putative cytochromes c were differentiated on gels in ATCC 33020 cells grown on ferrous iron or sulfur. All these cytochromes were associated with the inner or the outer membranes. Lower levels of total cytochromes c were observed in sulfur- than in ferrous iron-grown cells. One cytochrome c was specific for sulfur conditions while three were specific for iron conditions, suggesting that cytochrome c synthesis is modulated depending on the electron donor.     

嗜酸氧化亚铁硫杆菌doxDA操纵元的鉴定与分析

本文利用RT-PCR方法从转录水平上分别对A.ferrooxidans ATCC 23270基因组中可能编码硫酸盐-硫代硫酸盐结合蛋白基因sbp、膜结合硫代硫酸盐-辅酶Q氧化还原酶基因doxDA以及类硫氰酸酶基因p21等开放阅读框所在的基因座之间的联系进行了鉴定和分析,结果表明它们分别从属于预测的doxDA-1操纵元和doxDA-2操纵元.在此基础上,本文对doxDA操纵元的可能启动子序列也进行了预测和分析.     

固定化Acidithiobacillus ferrooxidans对Fe2+氧化及其生物反应器研究进展

Acidithiobacillus ferrooxidans 对Fe2+的生物氧化是一个非常重要的反应过程, 在生物浸矿、H2S等废气的脱硫、含重金属污泥和酸性矿坑废水的处理等领域有着重要的应用。近些年来,大量的研究主要集中A. ferrooxidans及其反应过程等方面,然而,A. ferrooxidans对Fe2+的催化氧化速率缓慢和稳定性欠佳等问题仍然限制了其商业应用。因此,对A. ferrooxidans的固定化及其生物反应器研究是该技术进一步发展的关键。本文评述了A. ferrooxidans最新应用、存在的问题和解决办法,重点比较了目前文献中报道的各种A. ferrooxidans固定材料、方法,并对目前采用的各种固定化A. ferrooxidans生物反应系统的效率和结构等方面进行了讨论和分析。     

嗜酸氧化亚铁硫杆菌的高效培养及浸出黄铜矿初探

采用向硫化矿培养基中补加FeSO4的方式以维持Fe2+ 浓度为4～8 g/L,可使嗜酸氧化亚铁硫杆菌菌浓在培养39 h时达到6.25×108 cells/mL,并在比生长速率几乎不降低的前提下提高了转化率和生产强度.然后对低氧化还原电位下低品位黄铜矿的浸出进行初步研究,结果表明经过30 d浸出,铜的浸出率可达28.5%...     

Sulfur Species Investigation in Extra- and Intracellular Sulfur Globules of Acidithiobacillus ferrooxidans and Acidithiobacillus caldus

The sulfur chemical speciation in extracellular and intracellular sulfur globules of Acidithiobacillus ferrooxidans and Acidithiobacillus caldus were investigated with an integrated approach including scanning electron microscopy, transmission electron microscopy, energy dispersive spectroscopy and sulfur K-edge X-ray absorption near edge structure spectroscopy (XANES). The results indicated that both strains can accumulate extracellular sulfur globules when grown on thiosulfate, and the major sulfur chemical speciation of which were S₈ for A. ferrooxidans and mixture of ring sulfur and polythionate for A. caldus, respectively. In contrast, A. ferrooxidans can accumulate both linear sulfur and S₈ internally when grown with sulfur powder and thiosulfate, whereas A. caldus did not accumulate intracellular sulfur globules. In addition, the fitted results of sulfur K-edge XANES spectra indicated that the reduced glutathione (containing thiols groups) were involved in sulfur bio-oxidation of both strains and the tetrathionate were the intermediate products during thiosulfate metabolism by two strains.     

嗜酸氧化亚铁硫杆菌ISC铁硫簇系统的合成

【目的】铁硫簇是最古老的一种氧化还原中心,它普遍存在于所有生命体内,在光合作用、呼吸作用和固氮作用这三个地球生命最基本的代谢途径中扮演着重要的角色。【方法】以嗜酸氧化亚铁硫杆菌(A.ferrooxidans ATCC 23270)基因组为模板,克隆表达其ISC铁硫簇组装的3个核心蛋白,IscS(半胱氨酸脱硫酶蛋白)、IscU(支架蛋白)和IscA(铁供体蛋白)。【结果】研究发现IscS能催化半胱氨酸脱硫,为铁硫簇的组装提供硫,支架蛋白IscU不具备结合铁的能力,IscA具有较强的铁结合能力。【结论】铁硫簇体外组装证明Fe-IscA在体外能将结合的铁传递给IscS,并在IscU上进行铁硫簇的组装。     

固体平板磁泳分离细菌新方法的研究

氧化亚铁硫杆菌（Acidithiobacillus ferrooxidans）能够在胞内形成电子致密的磁性颗粒,它的这种特性使利用氧化亚铁硫杆菌合成生物纳米磁性材料成为了可能。本课题组为了筛选出合成磁性颗粒能力强的菌株,对原有的液体磁泳进行了改进,采用了新的固体平板磁泳方法来筛选纯化目的菌株。经过磁泳分离后,细菌中含磁性颗粒的细胞比例由原始菌群的30％上升到90％,胞内含有的磁颗粒数目也由1~2颗增加至2~5颗,筛选得到的细菌在人工磁场下会进行趋磁运动。实验结果表明,氧化亚铁硫杆菌具有较弱的趋磁性,在人工磁场下会进行趋磁运动,但仅在地磁场作用下不能定向运动,利用固体平板磁泳筛选纯化含有磁性颗粒的氧化亚铁硫杆菌的方法是切实可行的,磁泳分离技术的进一步完善和改进为传统的微生物菌种分离提供了新的途径,为研究纯氧化亚铁硫杆菌菌株胞内磁性颗粒的形成条件及机理提供了前提条件,也为今后从浸矿细菌中分离筛选更多的含有磁性颗粒的菌株打下基础。     

Purification and Some Properties of Thiosulfate Dehydrogenase from Acidithiobacillus ferrooxidans

Abstract

Thiosulfate dehydrogenase was purified from Acidithiobacillus ferrooxidans using three purification steps. The purification procedure involved ammonium sulfate fractionation, ion‐exchange chromatography, and gel permeation chromatography. Specific activity of the purified enzyme (after IEC) was 3.26 nkat/mg, and yield of the enzyme was 78%. The purity of the enzyme was checked by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The enzyme is a tetramer composed of four probably identical subunits of relative molecular weight 45,000. The pH optimum of the enzyme reaction in the direction of substrate oxidation was found to be 3.0. The isoelectric point of the enzyme was 8.3. Enzyme activity was found to be particularly sensitive to the histidine‐selective reagent diethylpyrocarbonate. Reagents selective for arginine, cysteine, and tryptophane had no effect on enzyme activity.     

生物浸出系统中Acidithiobacillus ferrooxidans对雄黄表面改性研究

【目的】研究Acidithiobacillus ferrooxidans BY-3对雄黄表面改性作用,为进一步研究雄黄的生物炮制技术提供实验基础与理论依据。【方法】在4组生物浸出体系中(每组包含100 mL无亚铁离子的9K培养基和0.500 g雄黄):第1组无添加;第2组添加4.469 g硫酸亚铁;第3组添加0.100 g硫粉;第4组加入4.469 g硫酸亚铁和0.100 g硫粉。在上述4组中使用A.ferrooxidans BY-3对雄黄进行生物浸出。浸出前后雄黄表面形貌及元素变化,使用扫描电镜(SEM)与能谱仪(EDS)、X-射线衍射(XRD)、拉曼光谱(Raman)、电感耦合等离子体原子发射光谱仪(ICP-AES)进行分析。【结果】4组浸出体系均发现A.ferrooxidans BY-3粘附于雄黄表面以此来产生直接作用。含Fe2+的浸出体系中雄黄表面产生非常明显的变化,含硫的浸出体系中雄黄表面变化不明显;只有Fe2+存在的浸出体系中As/S比率增高,而其余3组浸出体系中As/S比率均明显下降;另外,改性雄黄的表面存在黄钾铁矾、硫、赤铁矿、针铁矿和磁铁矿等,但未检测到砷华(As2O3)与副雄黄(Pararealgar)。【结论】A.ferrooxidans对雄黄改性具有重要作用。Fe2+对雄黄的改性具有促进作用,而硫对雄黄的改性具有抑制作用。雄黄改性前后的物化分析结果证实了生物浸出技术可有效解决传统方法制备雄黄及贮存过程中氧化和光化问题。     

Shotgun proteomics of human bile in hilar cholangiocarcinoma

The need to find biomarkers for hepatobiliary diseases including cholangiocarcinoma (CCA) has led to an interest in using bile as a proximal fluid in biomarker discovery experiments, although there are inherent challenges both in its acquisition and analysis. The study described here greatly extends previous studies that have started to characterise the bile proteome. Bile from four patients with hilar CCA was depleted of albumin and immunoglobulin G and analysed by GeLC-MS/MS. The number of proteins identified per bile sample was between 378 and 741. Overall, the products of 813 unique genes were identified, considerably extending current knowledge of the malignant bile proteome. Of these, 268 were present in at least 3 out of 4 patients. This data set represents the largest catalogue of bile proteins to date and together with other studies in the literature constitutes an important prelude to the potential promise of expression proteomics and subsequent validation studies in CCA biomarker discovery.     

Inter- and intraspecific genomic variability of the 16S-23S intergenic spacer regions (ISR) in representatives of Acidithiobacillus thiooxidans and Acidithiobacillus ferrooxidans

The complete sequences of 32 intergenic spacer regions (ISR) from Acidithiobacillus strains, including 29 field strains isolated from coal, copper, molybdenum mine wastes or sediment of different geoclimatic regions in China, reference strain ATCC19859 and the type strains of the two species were determined. These data, together with other sequences available in the GenBank database, were used to carry out the first detailed assessment of the inter- and intraspecific genomic variability of the ISR sequences and to infer phylogenetic relationships within the genus. The total length of the 16S-23S rRNA intergenic spacer regions of the Acidithiobacillus thiooxidans and Acidithiobacillus ferrooxidans strains ranged from 451 to 490 bp, and from 434 to 456 bp, respectively. The degree of intrageneric ISR sequence similarity was higher than the degree of intergeneric similarity, and the overall similarity values of the ISRs varied from 60.49% to 84.71% between representatives of different species of the genus Acidithiobacillus. Sequences from the spacer of the A. thiooxidans and A. ferrooxidans strains ranged from 86.71% to 99.56% and 92.36% to 100% similarity, respectively. All Acidithiobacillus strains were separated into three phylogenetic major clusters and seven phylogenetic groups. ISR may be a potential target for the development of in situ hybridization probe aimed at accurately detecting acidithiobacilli in the various acidic environments.     

Bioadsorption of arsenic from aqueous solution by the extremophilic bacterium Acidithiobacillus ferrooxidans DLC-5

The bioadsorption of heavy metal ions to process industrial and solid wastes is an attractive technology from an economical and environmental point of view. This study investigated the equilibrium, thermodynamics and bioadsorption characteristics of arsenite (iAs^III) and dimethylarsinate (DMA^V) by Acidithiobacillus ferrooxidans (A. ferrooxidans) DLC-5 in aqueous solution. Optimum bioadsorption conditions were determined by identifying the optimum temperature, pH, biomass dosage, initial arsenic concentration and contact time. The equilibrium data were then applied to Langmuir and Freundlich isotherm models. The results indicated that the bioadsorption processes for both iAs^III and DMA^V involved pseudo-second-order kinetics. Additionally, the bioadsorption of iAs^III and DMA^V by A. ferrooxidans DLC-5 was feasible, spontaneous and endothermic under the tested conditions. Fourier transform infrared spectroscopy (FT-IR) showed that –OH and –NH groups were involved in the bioadsorption process. A. ferrooxidans DLC-5 demonstrates potential for use in removing arsenic from aqueous solutions, especially those with very low arsenic concentrations.     

葡萄糖对嗜酸氧化亚铁硫杆菌与Acidiphilium acidophilum共培养的影响

【目的】深入了解自养的嗜酸氧化亚铁硫杆菌(Acidithiobacillus ferrooxidans)与异养的Acidiphilium acidophilum之间的协同作用, 为嗜酸异养微生物在生物浸出体系和酸性矿坑水(AMD)等极端酸性环境中的生态功能研究提供基础, 并为AMD环境的修复提供参考。【方法】应用实时荧光定量PCR (RT-qPCR)及特异性引物, 定量At. ferrooxidans与Aph. acidophilum在类似自然状态下的共培养物受葡萄糖抑制时的生物量变化, 同时检测其生长过程中Fe2+氧化和pH值的变化。【结果】无论是否加入葡萄糖, 共培养对Fe2+氧化的效率均较At. ferrooxidans纯培养高。当葡萄糖浓度为5 g/L时, At. ferrooxidans纯培养失去对Fe2+的氧化能力, 而共培养仍能在100 h内将所有的Fe2+氧化完, 且加入葡萄糖越多的培养体系氧化终点的pH值也越高。在不加入葡萄糖的条件下, At. ferrooxidans 与Aph. acidophilum 数量比在100:1的数量级, 表明以这两种菌为代表的自养菌和异养菌在自然条件下生物量的比例。无论纯培养还是共培养的At. ferrooxidans数量均随葡萄糖浓度的提高而减少, 且延滞期则变长; 而异养生长的Aph. acidophilum则相反。【结论】适合进行Fe2+氧化的At. ferrooxidans与Aph. acidophilum的数量比例范围应在100:1的数量级。由于Aph. acidophilum能促进At. ferrooxidans对亚铁的氧化, 并能缓解或消除葡萄糖对At. ferrooxidans的抑制, 所以不能以加入类似于葡萄糖的有机物作为AMD环境生物修复的手段。     

微生物接种密度和矿物收集时间对生物沥浸中次生铁矿物形成的影响

在嗜酸性氧化亚铁硫杆菌Acidithiobacillus ferrooxidans作用下, 污泥生物沥浸体系中常会有次生铁矿物形成, 这些矿物对污泥脱水和重金属溶出有重要影响。在FeSO4-K2SO4-H2O生物成矾临界点模拟生物沥浸过程, 考察了Acidithiobacillus ferrooxidans菌接种密度和矿物收集时间对次生铁矿物的影响。结果表明, 微生物接种密度和矿物收集时间对生物沥浸过程中次生铁矿物的重量及其类型均有一定影响, 随矿物收集时间的推迟, 溶液中含有的一价阳离子(如K+等)可导致施氏矿物向黄铁矾发生转变, 并成为影响铁矿物类型的主导因素。     

嗜酸异养菌对自养菌Acidithiobacillus ferrooxidans金属离子抗性和生物浸出的影响

【目的】了解嗜酸异养菌在诸如酸性矿坑水(AMD)和生物浸出体系等极端酸性环境中对浸矿微生物产生的影响。【方法】研究由嗜酸异养菌Acidiphilium acidophilum和自养菌Acidithiobacillus ferrooxidans经长期驯化后形成的共培养体系分别在Cd2+、Cu2+、Ni2+和Mg2+胁迫下的稳定性;并将此共培养体系应用于黄铁矿和低品位黄铜矿的生物浸出实验。【结果】在上述4种金属离子分别存在的条件下,异养菌Aph.acidophilum均能促进At.ferrooxidans对亚铁的氧化,提高其对能源利用的效率。共培养体系中的异养菌Aph.acidophilum使At.ferrooxidans对Cu2+的最大耐受浓度(MTC)由2.0 g/L提高到5.0 g/L,而且共培养的细胞数量与2.0 g/L Cu2+条件下生长的At.ferrooxidans纯培养相似。另外,共培养中的At.ferrooxidans对Mg2+的MTC也由12.0 g/L提高到17.0 g/L。生物浸出实验中嗜酸异养菌Aph.acidophilum促进了At.ferrooxidans对黄铁矿样品的浸出,浸出率较其纯培养提高了22.7%;但在含铁量较低的低品位黄铜矿浸出体系中共培养和At.ferrooxidans纯培养的浸出率均低于33%。在加入2.0 g/L Fe2+的低品位黄铜矿浸出体系中,共培养和At.ferrooxidans纯培养的浸出率均得到提高,分别达到52.22%和41.27%。【结论】以上结果表明,Aph.acidophilum与At.ferrooxidans共培养在一定的环境胁迫下仍能保持其稳定性并完成各自的生态功能,并且嗜酸异养菌Aph.acidophilum适合在含铁量较高的浸出体系中与铁氧化细菌共同作用来提高生物浸出的效率。