Structure at 2.7 Å resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment

The aa3 type cytochrome c oxidase consisting of the core subunits I and II only was isolated from the soil bacterium Paracoccus denitrificans and crystallized as complex with a monoclonal antibody Fv fragment. Crystals could be grown in the presence of a number of different nonionic detergents. However, only undecyl-β-d-maltoside and cyclohexyl-hexyl-β-d-maltoside yielded well-ordered crystals suitable for high resolution x-ray crystallographic studies. The crystals belong to space group P212121 and diffract x-rays to at least 2.5 Å (1 Å = 0.1 nm) resolution using synchrotron radiation. The structure was determined to a resolution of 2.7 Å using molecular replacement and refined to a crystallographic R-factor of 20.5% (Rfree = 25.9%). The refined model includes subunits I and II and the 2 chains of the Fv fragment, 2 heme A molecules, 3 copper atoms, and 1 Mg/Mn atom, a new metal (Ca) binding site, 52 tentatively identified water molecules, and 9 detergent molecules. Only four of the water molecules are located in the cytoplasmic half of cytochrome c oxidase. Most of them are near the interface of subunits I and II. Several waters form a hydrogen-bonded cluster, including the heme propionates and the Mg/Mn binding site. The Fv fragment binds to the periplasmic polar domain of subunit II and is critically involved in the formation of the crystal lattice. The crystallization procedure is well reproducible and will allow for the analysis of the structures of mechanistically interesting mutant cytochrome c oxidases.

The microbiological destruction of thiocyanate in activated sludge plants treating coke oven effluent

The treatment of effluents produced during the manufacture of metallurgical coke is normally carried out using the activated sludge process. The efficiency of activated sludges in purifying coke oven effluent depends largely on the maintenance of species of micro-organisms which destroy thiocyanate. The composition, production, toxicity and treatment of coke oven effluent at Corby steelworks are described. A review is presented which follows the progress made towards identifying and monitoring the species of bacteria which destroy thiocyanate in biological treatment plants purifying coke oven effluents. In the present study a search for bacteria capable of destroying thiocyanate led to the isolation of a species of bacteria, identified as Pseudomonas putida, which destroyed thiocyanate in the presence of succinate; this species had not previously been reported to use thiocyanate. Washed cell suspensions of P. putida destroyed phenol and thiocyanate simultaneously and thiocyanate destruction was not suppressed by pyridine, aniline or catechol at the highest concentrations normally encountered in coke oven effluent. The isolate has been included, as N.C.I.B. 11198, in the National Collection of Industrial Bacteria, Torrey Research Station, Aberdeen. Three other isolates, identified as Achromobacter sp., Thiobacillus thioparus and T. denitrificans, were also confirmed to destroy thi.ocyanate. A technique has been developed for monitoring populations of different species of bacteria in activated sludges. Application of this technique to laboratory scale and full scale treatment plants at Corby showed that thiobacilli were usually not detected; thiobacilli were el~inated during the commissioning period of the full scale plant. However experiments using a laboratory scale plant indicated that during a period of three weeks an increase in the numbers of thiobacilli might have contributed to an improvement in plant performance. Factors which might have facilitated the development of thiobacilli are discussed. Large numbers of fluorescent pseudomonads capable of using thiocyanate were sometimes detected in the laboratory scale plant. The possibility is considered that catechol or other organic compounds in the feed-liquor might have stimulated fluorescent pseudmonads. Experiments using the laboratory scale plant confirmed that deteriorations in the efficiency of thiocyanate destruction were sometimes caused by bulking sludges, due to the excessive growth of fungal floes. Increased dilution of the coke oven effluent was a successful remedy to this difficulty. The optimum operating conditions recommended by the manufacturer of the full scale activated sludge plant at Corby are assessed and the role of bacterial monitoring in a programme of regular monitoring tests is discussed in relation to the operation of activated sludge plants treating coke oven effluents.

Estimation of mineral-adhered biomass of Thiobacillusferrooxidans by protein assay-some problems and remedies

Enumeration of adhered cells of Thiobacillus ferrooxidans on sulphide minerals through protein assay poses problems due to interference from dissolved mineral constituents. The manner in which sulphide minerals such as pyrite, chalcopyrite, sphalerite, arsenopyrite and pyrrhotite interfere with bacterial protein estimation is demonstrated. Such interferences can be minimised either through dilution or addition of H2O2 to the filtrate after hot alkaline digestion of the biotreated mineral samples.

Bioleaching of sulphides under applied potentials

The influence of applied DC potentials on the activity and growth of Thiobacillus ferrooxidans, as well as on the dissolution behaviour of some base metal sulphides is discussed with reference to bioleaching. Selective bioleaching of zinc from sphalerite could be achieved under an applied potential of −500 mV (saturated calomel electrode) from binary mineral mixtures containing the zinc mineral and chalcopyrite or pyrite. On the other hand, bioleaching of pyrite and chalcopyrite was found to be enhanced under positive potentials of +400 mV and +600 mV, respectively. Probable mechanisms in the electrobioleaching of sulphides are examined with respect to galvanic, microbiological and applied potential effects.

Electrobioleaching of base metal sulfides

Bioleaching of base metal sulfides, such as pyrite, chalcopyrite, and sphalerite, under the influence of applied direct current (DC) potentials is discussed. Contributions toward mineral dissolution from three effects, namely, galvanic, applied potential, and microbiological, are analyzed and compared. Sphalerite could be selectively bioleached in the presence of Thiobacillus ferrooxidans under an applied potential of -500 mV (SCE) from mixed sulfides containing sphalerite, pyrite, and chalcopyrite. Bacterial activity and growth were found to be promoted under electrobioleaching conditions. Probable mechanisms involved in the bioleaching of different sulfides under positive and negative applied potentials are discussed.

Some microbiological aspects of bauxite mineralization and beneficiation

A microbial survey of Jamnagar bauxite mines in Gujarat, India, revealed the indigenous presence of a variety of autotrophic and heterotrophic bacteria and fungi associated with the ore body and water ponds in the vicinity. Among these, bacteria belonging to the genera Thiobacillus, Bacillus and Pseudomonas are implicated in the weathering of aluminosilicates; the precipitation of iron oxyhydroxides; the dissolution and conversion of alkaline metal species; and the formation of alumina, silica and calcite minerals. Fungi belonging to the genus Cladosporium can reduce ferric iron and dissolve alumina silicates. Biogenesis thus plays a significant role in bauxite mineralization. Various types of bacteria and fungi, such as Bacillus polymyxa, Bacillus coagulans and Aspergillus niger, were found to be efficient in significant calcium solubilization and partial iron removal from bauxite ore. Probable mechanisms in the biobeneficiation process are analyzed. Biobeneficiation is shown to be an effective technique for the removal of iron and calcium from bauxite ores for use in refractories and ceramics.

Development of a clean bioelectrochemical process for leaching of ocean manganese nodules

Through the application of negative reduction potential significant reduction of manganic and iron oxides in the ocean manganese nodules can be achieved, liberating the occluded copper, nickel and cobalt for easy dissolution in an acid medium. Electroleaching and electrobioleaching of ocean manganese nodules in the presence of Thiobacillus ferrooxidans and Thiobacillus thiooxidans at the above negative applied dc potentials resulted in significant dissolution of copper, nickel and cobalt in 1 M H2SO4. The role of galvanic interactions in the bioleaching of ocean manganese nodules in the presence of T thiooxidans is also discussed, (C) 2002 Published by Elsevier Science Ltd.

Electrochemical aspects of leaching of ocean nodules in the presence and absence of microorganisms

instead of using chemical-reducing agents to facilitate the reduction and dissolution of manganese and iron oxide in the ocean nodule, electrochemical reduction based on two approaches, namely, cathodic polarization and galvanic interaction, can also be considered as attractive alternatives. Galvanic leaching of ocean nodules in the presence of pyrite and pyrolusite for complete recovery of Cu, Ni and Co has been discussed. The key for successful and efficient dissolution of copper, nickel and cobalt from ocean nodules depends on prior reduction of the manganese and ferric oxides with which the above valuable nonferrous metals are interlocked. Polarization studies using a slurry electrode system indicated that maximum dissolution of iron and manganese due to electrochemical reduction occurred at negative DC potentials of -600 mV (SCE) and -1400 mV (SCE). The present work is also relevant to galvanic bioleaching of ocean nodules using autotrophic microorganisms, such as Thiobacillus ferrooxidans and T thiooxidans, which resulted in significant dissolution of copper, nickel and cobalt at the expense of microbiologically generated acids. Various electrochemical and biochemical mechanisms are outlined and the electroleaching and galvanic processes so developed are shown to yield almost complete dissolution of all metal values. (C) 2002 Elsevier Science B.V. All rights reserved.

Strategies for efficient start-up of continuous biooxidation process for refractory gold ores

Strategies for efficient start-up of a continuous process for biooxidation of refractory gold ore and concentrate obtained from Hutti, Gold Mines Limited (HGML), India are discussed in this work. The biooxidation of the concentrate at high pulp density (10%) with wild strain of Thiobacillus ferrooxidans isolated from HGML mines is characterized by significant lag phase (20 days) and incomplete oxidation (35%) even after prolonged operation (60 days). Two strategies, biooxidation with concentrate adapted cells and a step leaching strategy, in which the pulp density is progressively increased from 2% to 10% were considered and the latter resulted in efficient biooxidation of concentrate. Conversion of such a process from batch to continuous operation is shown to result in complete biooxidation of the concentrate and gold extraction efficiency in excess of 90%. (C) 2002 Elsevier Science Ltd. All rights reserved.

Electrochemical and electron transfer investigations of copper proteins

A study of the pH and temperature dependence of the redox potentials of azurins from five species of bacteria has been performed. The variations in the potentials with pH have been interpreted in terms of electrostatic interactions between the copper site and titrating histidine residues, including the effects of substitutions in the amino acid sequences of the proteins on the electrostatic interactions. A comparison of the observed pH dependences with predictions based on histidine pK_a values known for Pseudomonas aeruginosa (Pae), Alcaligenes denitrificans (Ade), and Alcaligenes faecalis (Afa) azurins indicates that the Pae and Ade redox potentials exhibit pH dependences in line with electrostatic arguments, while Afa azurin exhibits more complex behavior. Redox enthalpies and entropies for four of the azurins at low and high pH values have also been obtained. Based on these results in conjuction with the variable pH experiments, it appears that Bordetella bronchiseptica azurin may undergo a more substantial conformational change with pH than has been observed for other species of azurin.

The temperature dependence of the redox potential of bovine erythrocyte superoxide dismutase (SOD) has been determined at pH 7.0, with potassium ferricyanide as the mediator. The following thermodynamic parameters have been obtained (T = 25°C): E°' = 403±5 mV vs. NHE, ΔG°' = -9.31 kcal/mol, ΔH°' = -21.4 kcal/mol, ΔS°' = -40.7 eu, ΔS°'_(rc) = -25.1 eu. It is apparent from these results that ΔH°', rather than ΔS°', is the dominant factor in establishing the high redox potential of SOD. The large negative enthalpy of reduction may also reflect the factors which give SOD its high specificity toward reduction and oxidation by superoxide.

Physical characterization of the rack effect and hydrogen bond networks in blue copper proteins

A summary of previous research is presented that indicates that the purpose of a blue copper protein's fold and hydrogen bond network, aka, the rack effect, enforce a copper(II) geometry around the copper(I) ion in the metal site. In several blue copper proteins, the C-terminal histidine ligand becomes protonated and detaches from the copper in the reduced forms. Mutants of amicyanin from Paracoccus denitrificans were made to alter the hydrogen bond network and quantify the rack effect by pK_a shifts.

The pK_a's of mutant amicyanins have been measured by pH-dependent electrochemistry. P94F and P94A mutations loosen the Northern loop, allowing the reduced copper to adopt a relaxed conformation: the ability to relax drives the reduction potentials up. The measured potentials are 265 (wild type), 380 (P94A), and 415 (P94F) mV vs. NHE. The measured pK_a's are 7.0 (wild type), 6.3 (P94A), and 5.0 (P94F). The additional hydrogen bond to the thiolate in the mutants is indicated by a red-shift in the blue copper absorption and an increase in the parallel hyperfine splitting in the EPR spectrum. This hydrogen bond is invoked as the cause for the increased stability of the C-terminal imidazole.

Melting curves give a measure of the thermal stability of the protein. A thermodynamic intermediate with pH-dependent reversibility is revealed. Comparisons with the electrochemistry and apoamicyanin suggest that the intermediate involves the region of the protein near the metal site. This region is destabilized in the P94F mutant; coupled with the evidence that the imidazole is stabilized under the same conditions confirms an original concept of the rack effect: a high energy configuration is stabilized at a cost to the rest of the protein.

Achromobacter xylosoxidans na fibrose cística: infecção crônica e disseminação clonal

A mortalidade na Fibrose Cística (FC) é decorrente de infecções pulmonares causadas comumente por: Pseudomonas aeruginosa, Staphylococcus aureus e espécies do Complexo Burkholderia cepacia (CBc). Mais recentemente, tem sido observada a emergência de BGN-NF raros, como Achromobacter xylosoxidans, porém, sua prevalência, potencial de transmissão e significado clínico são desconhecidos. O objetivo deste trabalho foi verificar a ocorrência de colonização crônica por A. xylosoxidans e avaliar a possibilidade de transmissão cruzada entre os pacientes acompanhados em dois centros de referência na cidade do Rio de Janeiro. Foram incluídos 39 pacientes com FC, com pelo menos uma cultura positiva para o gênero Achromobacter spp., em um total de 897 analisadas, do período de janeiro de 2003 a dezembro de 2008. A frequência de isolamento de Achromobacter spp. nas culturas analisadas foi de 14,5% (130 em 897 culturas). A maioria (n=122; 93,8%) foi identificada como A. xylosoxidans por testes fenotípicos e pelo sequenciamento do gene rrs que codifica o 16S rRNA. A análise do polimorfismo genético dos isolados de A. xylosoxidans pela técnica de PFGE, mostrou 22 grupos clonais. Destes, sete foram compartilhados entre pacientes distintos sugerindo transmissão cruzada. Apenas o clone G foi amplamente disseminado entre 56,4% dos pacientes estudados, sugerindo a possibilidade de um surto. Os 15 clones restantes constituíram-se em clones exclusivos por pacientes. Os cinco pacientes colonizados cronicamente por A. xylosoxidans mostraram a prevalência de clones únicos. Até o momento, este é o primeiro caso da ocorrência de surto por A. xylosoxidans em pacientes com Fibrose Cística. A. xylosoxidans é um microrganismo que vem se destacando em frequência e como um possível patógeno pulmonar nesses pacientes. Entretanto, até o momento os dados são insuficientes para avaliar a sua contribuição para a evolução da doença pulmonar. Estudos que busquem elucidar as características de A. xylosoxidans que o permitem colonizar persistentemente o pulmão dos pacientes com FC, bem como seu potencial de virulência, são necessários.

微生物法沥取重金属污泥中铬的研究

本文研究了两种微生物及其组合沥取、回收用微生物法治理电镀铬废水产生的铬污泥中的铬。铬污泥富含C、N、O，含铬量为13%， 经X-光电子能谱分析铬以三价态(氢氧化铬)存在。二种微生物分别从一酸性矿水和酸性污泥中分离筛选得到，经鉴定为硫杆菌属 (Thiobacillus Beijerinek)的两个不同种，一为氧化亚铁硫杆菌(Thiobacillu ferrooxidans, TF), 另一为氧化硫硫杆菌 (Thiobacillus thiooxidans, TT)。研究并比较了不同微生物对污泥中铬的沥取能力，结果表明，TT菌沥取铬效率最高。振荡、动 态淋滤、静置等沥取方式经过研究表明动态淋滤为最佳，室温条件下(15-20℃)，污泥浓度为20g/L时，总铬沥出率达60%时所需时 间：动态淋滤为48.5h，振荡和静置方式分别为91.22，81.6h。研究了不同温度、不同起始PH、不同污泥浓度及非成熟菌液对微生 物沥取能力的影响：(1) 沥取前期，温度对铬的沥出影响较大；微生物沥取反应基本属一级反应；温度与反应速率的关系基本符合 Arrhenius方程，但沥取后期这一特点并不突出。(2) 沥取液最适起始PH为菌液自然PH；PH值的人为改变将使铬的沥出大大降低。 (3) 污泥浓度与铬的沥出呈正相关，但浓度高于30g/L时，铬的沥出量不再增加。(4) 非成熟菌液沥出铬的能力较差，但沥取液中 微生物生长繁殖较为活跃。总结微生物沥取反应最佳沥取条件为：TT成熟菌液、污泥浓度10g/L、温度25-36℃、动态淋滤方式，此 时铬几乎可100%从污泥中沥出。经扫描电镜分析，沥取开始时，微生物紧密吸附于污泥颗粒表面上，表面紧密吸附为微生物发挥功 能提供了基础。微生物沥取污泥中铬的反应机理推测为：硫细菌代谢产硫酸或氧化Fe2+成Fe3+，利用酸，Fe3+ 及自身氧化酶系统 氧化污泥中Cr3+为Cr6+,Cr6+溶出结晶为CrO3。This paper has studied bioleaching and recovery of Chronium(Cr)from electroplating sludge by two consortum of bacteria and their combination, with sludge produced by microbiological process treating electroplating wastewater containing Cr as material. The share of Cr is 13% and its state is Cr (OH)3 in the sludge. One of the bacteria in the paper was isolated from acid sewage sludge and the other was from acid mineral water. The former was tested and determined as Thiobacillus ferroxidans(TF) and the latter was Thiobacillus thiooxidans(TT). Different microorganisms, responsible for the metal leaching activity, have great influence on the efficiency of leaching. The results showed that TT has biggest power. Experiments were conducted to examined effects of three different ways of leaching(Shaking, Down-leaching, Static-leaching). When temperature was in-door's (15-20℃)and concentration of the sludge was 20g/L, the bioleaching time required to reach 60% of Cr solubilization with the above three ways were 91.2, 48.5, 81.6h respectively. Down-leaching was proved to be the most efficient. The influence of different temperature, initial PH, concentration of the sludge and non-mature inoculum had been studied. The results obtained reveal that: (1) The variation of temperature is important during the time from initial to middle of leaching. The reaction of bioleaching belongs to first-order. The relation between the bioleaching rate constant(In k)and temerature can be expressed by Arrhenius function. (2) The fittest initial PH is the nature PH of mature inoculum. Any alteration with it could cause clearly negative effection. (3) The concentration of the sludge can make strong influence on the bioleaching efficiency. But when the concentration is above 30g/L, the increasing of Cr in the solution is little. (4) If non-mature inoculum acts as the bioleachin microorganism, little quantity of Cr would be gained from the sludge. But the micormass in the solution is very active. The results from electron microscope showed that microorganisms adhered to the surface of the sludge and the adherence was the first stage of the bioleaching. Some salts of Cr can be obtained afer the water of the bioleaching solution being evaporated. By analysing the results of experiment with X-Ray spectroscopy, the salt was identified as CrO3. The recovery rate of Cr is 78.4%.

Low rates of Pseudomonas aeruginosa misidentification in isolates from cystic fibrosis patients

Pseudomonas aeruginosa is an important cause of pulmonary infection in cystic fibrosis (CF). Its correct identification ensures effective patient management and infection control strategies. However, little is known about how often CF sputum isolates are falsely identified as P. aeruginosa. We used P. aeruginosa-specific duplex real-time PCR assays to determine if 2,267 P. aeruginosa sputum isolates from 561 CF patients were correctly identified by 17 Australian clinical microbiology laboratories. Misidentified isolates underwent further phenotypic tests, amplified rRNA gene restriction analysis, and partial 16S rRNA gene sequence analysis. Participating laboratories were surveyed on how they identified P. aeruginosa from CF sputum. Overall, 2,214 (97.7%) isolates from 531 (94.7%) CF patients were correctly identified as P. aeruginosa. Further testing with the API 20NE kit correctly identified only 34 (59%) of the misidentified isolates. Twelve (40%) patients had previously grown the misidentified species in their sputum. Achromobacter xylosoxidans (n = 21), Stenotrophomonas maltophilia (n = 15), and Inquilinus limosus (n = 4) were the species most commonly misidentified as P. aeruginosa. Overall, there were very low rates of P. aeruginosa misidentification among isolates from a broad cross section of Australian CF patients. Additional improvements are possible by undertaking a culture history review, noting colonial morphology, and performing stringent oxidase, DNase, and colistin susceptibility testing for all presumptive P. aeruginosa isolates. Isolates exhibiting atypical phenotypic features should be evaluated further by additional phenotypic or genotypic identification techniques.

The electron transfer complex between nitrous oxide reductase and its electron donors

J Biol Inorg Chem (2011) 16:1241–1254 DOI 10.1007/s00775-011-0812-9