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  • 1. Baker-Austin, Craig
    et al.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Life in acid: pH homeostasis in acidophiles.2007In: Trends Microbiol, ISSN 0966-842X, Vol. 15, no 4, p. 165-71Article in journal (Refereed)
    Abstract [en]

    Microorganisms that have a pH optimum for growth of less than pH 3 are termed "acidophiles". To grow at low pH, acidophiles must maintain a pH gradient of several pH units across the cellular membrane while producing ATP by the influx of protons through the F(0)F(1) ATPase. Recent advances in the biochemical analysis of acidophiles coupled to sequencing of several genomes have shed new insights into acidophile pH homeostatic mechanisms. Acidophiles seem to share distinctive structural and functional characteristics including a reversed membrane potential, highly impermeable cell membranes and a predominance of secondary transporters. Also, once protons enter the cytoplasm, methods are required to alleviate effects of a lowered internal pH. This review highlights recent insights regarding how acidophiles are able to survive and grow in these extreme conditions.

  • 2. Baker-Austin, Craig
    et al.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Wexler, Margaret
    Sawers, R Gary
    Bond, Philip L
    Molecular insight into extreme copper resistance in the extremophilic archaeon 'Ferroplasma acidarmanus' Fer1.2005In: Microbiology, ISSN 1350-0872, Vol. 151, no Pt 8, p. 2637-46Article in journal (Refereed)
    Abstract [en]

    'Ferroplasma acidarmanus' strain Fer1 is an extremely acidophilic archaeon involved in the genesis of acid mine drainage, and was isolated from copper-contaminated mine solutions at Iron Mountain, CA, USA. Here, the initial proteomic and molecular investigation of Cu(2+) resistance in this archaeon is presented. Analysis of Cu(2+) toxicity via batch growth experiments and inhibition of oxygen uptake in the presence of ferrous iron demonstrated that Fer1 can grow and respire in the presence of 20 g Cu(2+) l(-1). The Fer1 copper resistance (cop) loci [originally detected by Ettema, T. J. G., Huynen, M. A., de Vos, W. M. & van der Oost, J. Trends Biochem Sci 28, 170-173 (2003)] include genes encoding a putative transcriptional regulator (copY), a putative metal-binding chaperone (copZ) and a putative copper-transporting P-type ATPase (copB). Transcription analyses demonstrated that copZ and copB are co-transcribed, and transcript levels were increased significantly in response to exposure to high levels of Cu(2+), suggesting that the transport system is operating for copper efflux. Proteomic analysis of Fer1 cells exposed to Cu(2+) revealed the induction of stress proteins associated with protein folding and DNA repair (including RadA, thermosome and DnaK homologues), suggesting that 'Ferroplasma acidarmanus' Fer1 uses multiple mechanisms for resistance to high levels of copper.

  • 3. Baker-Austin, Craig
    et al.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Wexler, Margaret
    Sawers, R Gary
    Stemmler, Ann
    Rosen, Barry P
    Bond, Philip L
    Extreme arsenic resistance by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.2007In: Extremophiles, ISSN 1431-0651, Vol. 11, no 3, p. 425-34Article in journal (Refereed)
    Abstract [en]

    'Ferroplasma acidarmanus' Fer1 is an arsenic-hypertolerant acidophilic archaeon isolated from the Iron Mountain mine, California; a site characterized by heavy metals contamination. The presence of up to 10 g arsenate per litre [As(V); 133 mM] did not significantly reduce growth yields, whereas between 5 and 10 g arsenite per litre [As(III); 67-133 mM] significantly reduced the yield. Previous bioinformatic analysis indicates that 'F. acidarmanus' Fer1 has only two predicted genes involved in arsenic resistance and lacks a recognizable gene for an arsenate reductase. Biochemical analysis suggests that 'F. acidarmanus' Fer1 does not reduce arsenate indicating that 'F. acidarmanus' Fer1 has an alternative resistance mechanism to arsenate other than reduction to arsenite and efflux. Primer extension analysis of the putative ars transcriptional regulator (arsR) and efflux pump (arsB) demonstrated that these genes are co-transcribed, and expressed in response to arsenite, but not arsenate. Two-dimensional polyacrylamide gel electrophoresis analysis of 'F. acidarmanus' Fer1 cells exposed to arsenite revealed enhanced expression of proteins associated with protein refolding, including the thermosome Group II HSP60 family chaperonin and HSP70 DnaK type heat shock proteins. This report represents the first molecular and proteomic study of arsenic resistance in an acidophilic archaeon.

  • 4. Bijmans, Martijn F M
    et al.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Ennin, Frederick
    Lens, Piet N L
    Buisman, Cees J N
    Effect of sulfide removal on sulfate reduction at pH 5 in a hydrogen fed gas-lift bioreactor.2008In: Journal of Microbiology and Biotechnology, ISSN 1017-7825, E-ISSN 1738-8872, Vol. 18, no 11, p. 1809-18Article in journal (Refereed)
    Abstract [en]

    Biotechnological treatment of sulfate- and metal-ionscontaining acidic wastewaters from mining and metallurgical activities utilizes sulfate-reducing bacteria to produce sulfide that can subsequently precipitate metal ions. Reducing sulfate at a low pH has several advantages above neutrophilic sulfate reduction. This study describes the effect of sulfide removal on the reactor performance and microbial community in a high-rate sulfidogenic gas-lift bioreactor fed with hydrogen at a controlled internal pH of 5. Under sulfide removal conditions, 99% of the sulfate was converted at a hydraulic retention time of 24 h, reaching a volumetric activity as high as 51 mmol sulfate/l/d. Under nonsulfide removal conditions, <25% of the sulfate was converted at a hydraulic retention time of 24 h reaching volumetric activities of <13mmol sulfate/l/d. The absence of sulfide removal at a hydraulic retention time of 24 h resulted in an average H2S concentration of 18.2 mM (584 mg S/l). The incomplete sulfate removal was probably due to sulfide inhibition. Molecular phylogenetic analysis identified 11 separate 16S rRNA bands under sulfide stripping conditions, whereas under nonsulfide removal conditions only 4 separate 16S rRNA bands were found. This shows that a less diverse population was found in the presence of a high sulfide concentration.

  • 5. Bijmans, MFM
    et al.
    de Vries, E
    Yang, Chun-Hui
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Buisman, CJN
    Lens, PNL
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Sulfate reduction at pH 4.0 for treatment of process and wastewaters2010In: Biotechnology progress (Print), ISSN 8756-7938, E-ISSN 1520-6033, Vol. 26, no 4, p. 1029-1037Article in journal (Refereed)
    Abstract [en]

    Acidic industrial process and wastewaters often contain high sulfate and metal concentrations and their direct biological treatment is thus far not possible as biological processes at pH < 5 have been neglected. Sulfate-reducing bacteria convert sulfate to sulfide that can subsequently be used to recover metals as metal-sulfides precipitate. This study reports on high-rate sulfate reduction with a mixed microbial community at pH 4.0 and 4.5 with hydrogen and/or formate as electron donors. The maximum sulfate reducing activity at pH 4.0 was sustained for over 40 days with a specific activity 500-fold greater than previously reported values: 151 mmol sulfate reduced/L reactor liquid per day with a maximum specific activity of 84 mmol sulfate per gram of volatile suspended solids per day. The biomass yield gradually decreased from 38 to 0.4 g volatile suspended solids per kilogram of sulfate when decreasing the reactor pH from pH 6 to 4. The microorganisms had a high maintenance requirement probably due maintaining pH homeostasis and the toxicity of sulfide at low pH. The microbial community diversity in the pH 4.0 membrane bioreactor decreased over time, while the diversity of the sulfate reducing community increased. Thus, a specialized microbial community containing a lower proportion of microorganisms capable of activity at pH 4 developed in the reactor compared with those present at the start of the experiment. The 16S rRNA genes identified from the pH 4.0 grown mixed culture were most similar to those of Desulfovibrio species and Desulfosporosinus sp. M1. (C) 2010 American Institute of Chemical Engineers Biotechnol. Prog., 26: 1029-1037, 2010

  • 6.
    Dar, Shabir A
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Bijmans, Martijn F M
    Dinkla, Inez J T
    Geurkink, Bert
    Lens, Piet N L
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Population dynamics of a single-stage sulfidogenic bioreactor treating synthetic zinc-containing waste streams2009In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 58, no 3, p. 529-537Article in journal (Refereed)
    Abstract [en]

    Waste streams from industrial processes such as metal smelting or mining contain high concentrations of sulfate and metals with low pH. Dissimilatory sulfate reduction carried out by sulfate-reducing bacteria (SRB) at low pH can combine sulfate reduction with metal-sulfide precipitation and thus open possibilities for selective metal recovery. This study investigates the microbial diversity and population changes of a single-stage sulfidogenic gas-lift bioreactor treating synthetic zinc-rich waste water at pH 5.5 by denaturing gradient gel electrophoresis of 16S rRNA gene fragments and quantitative polymerase chain reaction. The results indicate the presence of a diverse range of phylogenetic groups with the predominant microbial populations belonging to the Desulfovibrionaceae from delta-Proteobacteria. Desulfovibrio desulfuricans-like populations were the most abundant among the SRB during the three stable phases of varying sulfide and zinc concentrations and increased from 13% to 54% of the total bacterial populations over time. The second largest group was Desulfovibrio marrakechensis-like SRB that increased from 1% to about 10% with decreasing sulfide concentrations. Desulfovibrio aminophilus-like populations were the only SRB to decrease in numbers with decreasing sulfide concentrations. However, their population was <1% of the total bacterial population in the reactor at all analyzed time points. The number of dissimilatory sulfate reductase (DsrA) gene copies per number of SRB cells decreased from 3.5 to 2 DsrA copies when the sulfide concentration was reduced, suggesting that the cells' sulfate-reducing capacity was also lowered. This study has identified the species present in a single-stage sulfidogenic bioreactor treating zinc-rich wastewater at low pH and provides insights into the microbial ecology of this biotechnological process.

  • 7.
    Dopson, Mark
    et al.
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Baker-Austin, Craig
    Bond, Philip
    Towards determining details of anaerobic growth coupled to ferric iron reduction by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.2007In: Extremophiles, ISSN 1431-0651, Vol. 11, no 1, p. 159-68Article in journal (Refereed)
    Abstract [en]

    Elucidation of the different growth states of Ferroplasma species is crucial in understanding the cycling of iron in acid leaching sites. Therefore, a proteomic and biochemical study of anaerobic growth in 'Ferroplasma acidarmanus' Fer1 has been carried out. Anaerobic growth in Ferroplasma spp. occurred by coupling oxidation of organic carbon with the reduction of Fe(3+); but sulfate, nitrate, sulfite, thiosulfate, and arsenate were not utilized as electron acceptors. Rates of Fe(3+) reduction were similar to other acidophilic chemoorganotrophs. Analysis of the 'F. acidarmanus' Fer1 proteome by 2-dimensional polyacrylamide gel electrophoresis revealed ten key proteins linked with central metabolic pathways > or =4 fold up-regulated during anaerobic growth. These included proteins putatively identified as associated with the reductive tricarboxylic acid pathway used for anaerobic energy production, and others including a putative flavoprotein involved in electron transport. Inhibition of anaerobic growth and Fe(3+) reduction by inhibitors suggests the involvement of electron transport in Fe(3+)reduction. This study has increased the knowledge of anaerobic growth in this biotechnologically and environmentally important acidophilic archaeon.

  • 8.
    Dopson, Mark
    et al.
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Baker-Austin, Craig
    Bond, Philip L
    Analysis of differential protein expression during growth states of Ferroplasma strains and insights into electron transport for iron oxidation.2005In: Microbiology, ISSN 1350-0872, Vol. 151, no Pt 12, p. 4127-37Article in journal (Refereed)
    Abstract [en]

    To investigate the metabolic biochemistry of iron-oxidizing extreme acidophiles, a proteomic analysis of chemomixotrophic and chemo-organotrophic growth, as well as protein expression in the absence of organic carbon, was carried out in Ferroplasma species. Electron transport chain inhibitor studies, spectrophotometric analysis and proteomic results suggest that oxidation of ferrous iron may be mediated by the blue copper-haem protein sulfocyanin and the derived electron passes to a cbb3 terminal electron acceptor. Despite previous suggestions of a putative carbon dioxide fixation pathway, no up-regulation of proteins typically associated with carbon dioxide fixation was evident during incubation in the absence of organic carbon. Although a lack of known carbon dioxide fixation proteins does not constitute proof, the results suggest that these strains are not autotrophic. Proteins putatively involved in central metabolic pathways, a probable sugar permease and flavoproteins were up-regulated during chemo-organotrophic growth in comparison to the protein complement during chemomixotrophic growth. These results reflect a higher energy demand to be derived from the organic carbon during chemo-organotrophic growth. Proteins with suggested function as central metabolic enzymes were expressed at higher levels during chemomixotrophic growth by Ferroplasma acidiphilum Y(T) compared to 'Ferroplasma acidarmanus' Fer1. This study addresses some of the biochemical and bioenergetic questions fundamental for survival of these organisms in extreme acid-leaching environments.

  • 9.
    Dopson, Mark
    et al.
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Baker-Austin, Craig
    Bond, Philip L
    First use of two-dimensional polyacrylamide gel electrophoresis to determine phylogenetic relationships.2004In: J Microbiol Methods, ISSN 0167-7012, Vol. 58, no 3, p. 297-302Article in journal (Refereed)
    Abstract [en]

    Methods for microbial classification are not always capable of distinguishing between isolates at the species level. We have previously characterised four Ferroplasma isolates that were >98.9% similar at the 16S rDNA level, the isolates showed marked phenotypic differences, and one isolate was borderline on the 70% species boundary from DNA-DNA similarity data. In this study we have used statistical comparisons of two-dimensional polyacylamide gel electrophoresis gels for classification of closely related isolates. From the protein profile similarities an un-rooted tree was constructed that was congruent with a tree derived from DNA-DNA similarities.

  • 10.
    Dopson, Mark
    et al.
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Baker-Austin, Craig
    Hind, Andrew
    Bowman, John P
    Bond, Philip L
    Characterization of Ferroplasma isolates and Ferroplasma acidarmanus sp. nov., extreme acidophiles from acid mine drainage and industrial bioleaching environments.2004In: Appl Environ Microbiol, ISSN 0099-2240, Vol. 70, no 4, p. 2079-88Article in journal (Refereed)
    Abstract [en]

    Three recently isolated extremely acidophilic archaeal strains have been shown to be phylogenetically similar to Ferroplasma acidiphilum Y(T) by 16S rRNA gene sequencing. All four Ferroplasma isolates were capable of growing chemoorganotrophically on yeast extract or a range of sugars and chemomixotrophically on ferrous iron and yeast extract or sugars, and isolate "Ferroplasma acidarmanus" Fer1(T) required much higher levels of organic carbon. All four isolates were facultative anaerobes, coupling chemoorganotrophic growth on yeast extract to the reduction of ferric iron. The temperature optima for the four isolates were between 35 and 42 degrees C and the pH optima were 1.0 to 1.7, and "F. acidarmanus" Fer1(T) was capable of growing at pH 0. The optimum yeast extract concentration for "F. acidarmanus" Fer1(T) was higher than that for the other three isolates. Phenotypic results suggested that isolate "F. acidarmanus" Fer1(T) is of a different species than the other three strains, and 16S rRNA sequence data, DNA-DNA similarity values, and two-dimensional polyacrylamide gel electrophoresis protein profiles clearly showed that strains DR1, MT17, and Y(T) group as a single species. "F. acidarmanus" Fer1(T) groups separately, and we propose the new species "F. acidarmanus" Fer1(T) sp. nov.

  • 11.
    Dopson, Mark
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Halinen, Anna-Kaisa
    Rahrmen, Nelli
    Boström, Dan
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics, Energy Technology and Thermal Process Chemistry.
    Sundkvist, Jan-Eric
    Riekkola-Vanhanen, Marja
    Kaksonen, Anna H.
    Puhakka, Jaakko A.
    Silicate mineral dissolution during heap bioleaching2008In: Biotechnology and Bioengineering, ISSN 0006-3592, E-ISSN 1097-0290, Vol. 99, no 4, p. 811-820Article in journal (Refereed)
    Abstract [en]

    Silicate minerals are present in association with metal sulfides in ores and their dissolution occurs when the sulfide minerals are bioleached in heaps for metal recovery. It has previously been suggested that silicate mineral dissolution can affect mineral bioleaching by acid consumption, release of trace elements, and increasing the viscosity of the teach solution. In this study, the effect of silicates present in three separate samples in conjunction with chalcopyrite and a complex multi-metal sulfide ore on heap bioleaching was evaluated in column bioreactors. Fe2+ oxidation was inhibited in columns containing chalcopyrite samples A and C that leached 1.79 and 1.11 mM fluoride, respectively but not in sample B that contained 0.14 mM fluoride. Microbial Fe2+ oxidation inhibition experiments containing elevated fluoride concentrations and measurements of fluoride release from the chalcopyrite ores supported that inhibition of Fe2+ oxidation during column leaching of two of the chalcopyrite ores was due to fluoride toxicity. Column bioleaching of the complex sulfide ore was carried out at various temperatures (7-50 degrees C) and pH values (1.5-3.0). Column leaching at pH 1.5 and 2.0 resulted in increased acid consumption rates and silicate dissolution such that it became difficult to filter the leach solutions and for the leach liquor to percolate through the column. However, column temperature (at pH 2.5) only had a minor effect on the acid consumption and silicate dissolution rates. This study demonstrates the potential negative impact of silicate mineral dissolution on heap bioleaching by microbial inhibition and liquid flow.

  • 12.
    Dopson, Mark
    et al.
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Halinen, Anna-Kaisa
    Rahunen, Nelli
    Ozkaya, Bestamin
    Sahinkaya, Erkan
    Kaksonen, Anna H
    Lindström, Börje
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Puhakka, Jaakko A
    Mineral and iron oxidation at low temperatures by pure and mixed cultures of acidophilic microorganisms.2007In: Biotechnol Bioeng, ISSN 0006-3592, Vol. 97, no 5, p. 1205-15Article in journal (Refereed)
    Abstract [en]

    An enrichment culture from a boreal sulfide mine environment containing a low-grade polymetallic ore was tested in column bioreactors for simulation of low temperature heap leaching. PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequencing revealed the enrichment culture contained an Acidithiobacillus ferrooxidans strain with high 16S rRNA gene similarity to the psychrotolerant strain SS3 and a mesophilic Leptospirillum ferrooxidans strain. As the mixed culture contained a strain that was within a clade with SS3, we used the SS3 pure culture to compare leaching rates with the At. ferrooxidans type strain in stirred tank reactors for mineral sulfide dissolution at various temperatures. The psychrotolerant strain SS3 catalyzed pyrite, pyrite/arsenopyrite, and chalcopyrite concentrate leaching. The rates were lower at 5 degrees C than at 30 degrees C, despite that all the available iron was in the oxidized form in the presence of At. ferrooxidans SS3. This suggests that although efficient At. ferrooxidans SS3 mediated biological oxidation of ferrous iron occurred, chemical oxidation of the sulfide minerals by ferric iron was rate limiting. In the column reactors, the leaching rates were much less affected by low temperatures than in the stirred tank reactors. A factor for the relatively high rates of mineral oxidation at 7 degrees C is that ferric iron remained in the soluble phase whereas, at 21 degrees C the ferric iron precipitated. Temperature gradient analysis of ferrous iron oxidation by this enrichment culture demonstrated two temperature optima for ferrous iron oxidation and that the mixed culture was capable of ferrous iron oxidation at 5 degrees C. (c) 2006 Wiley Periodicals, Inc.

  • 13.
    Dopson, Mark
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Kupka, Daniel
    Halinen, Anna-Kaisa
    Rahunen, Nelli
    Özkaya, Bestamin
    Sahinkaya, Erkan
    Rzhepishevska, Olena I
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Kaksonen, Anna H
    Karnachuk, Olia V
    Tuovinen, IH
    Puhakka, Jaakko A
    Iron oxidation and bioleaching potential at low temperatures2007In: Biohydrometallurgy: from the single cell to the environment / [ed] Axel Schippers, Zurich: Trans Tech Publications Inc., 2007, p. 578-578Conference paper (Refereed)
  • 14.
    Dopson, Mark
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Lindström, E Börje
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Analysis of community composition during moderately thermophilic bioleaching of pyrite, arsenical pyrite and chalcopyrite2004In: Microbial Ecology, Vol. 48, p. 19-28Article in journal (Other (popular science, discussion, etc.))
  • 15.
    Dopson, Mark
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Lövgren, Lars
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Boström, Dan
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics, Energy Technology and Thermal Process Chemistry.
    Silicate mineral dissolution in the presence of acidophilic microorganisms: implications for heap bioleaching2009In: Hydrometallurgy, ISSN 0304-386X, E-ISSN 1879-1158, Vol. 96, no 4, p. 288-293Article in journal (Refereed)
    Abstract [en]

    Silicate minerals are found with sulfide minerals and therefore, can be present during heap bioleaching for metal extraction. The weathering of silicate minerals by chemical and biological means is variable depending on the conditions and microorganisms tested. In low pH metal rich environments their dissolution can influence the solution chemistry by increasing pH, releasing toxic trace elements, and thickening of the leach liquor. The amenity of five silicate minerals to chemical and biological dissolution was tested in the presence of either ‘Ferroplasma acidarmanus’ Fer1 or Acidithiobacillus ferrooxidans with olivine and hornblende being the most and least amenable, respectively. A number of the silicates caused the pH of the leach liquor to increase including augite, biotite, hornblende, and olivine. For the silicate mineral olivine, the factors affecting magnesium dissolution included addition of microorganisms and Fe2+. XRD analysis identified secondary minerals in several of the experiments including jarosite from augite and hornblende when the medium contained Fe2+. Despite acidophiles preferentially attaching to sulfide minerals, the increase in iron coupled with very low Fe2+ concentrations present at the end of leaching during dissolution of biotite, olivine, hornblende, and microcline suggested that these minerals supported growth. Weathering of the tested silicates would affect heap bioleaching by increasing the pH with olivine, fluoride release from biotite, and production of jarosite during augite and hornblende dissolution that may have caused passivation. These data have increased knowledge of silicate weathering under bioleaching conditions and provided insights into the effects on solution chemistry during heap bioleaching.

  • 16. Dopson, Mark
    et al.
    Ossandon, Francisco J.
    Lövgren, Lars
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Holmes, David S.
    Metal resistance or tolerance?: Acidophiles confront high metal loads via both abiotic and biotic mechanisms2014In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 5, p. 157-Article in journal (Refereed)
    Abstract [en]

    All metals are toxic at high concentrations and consequently their intracellular concentrations must be regulated. Extremely acidophilic microorganisms have an optimum growth of pH <3 and proliferate in natural and anthropogenic low pH environments. Some acidophiles are involved in the catalysis of sulfide mineral dissolution, resulting in high concentrations of metals in solution. Acidophiles are often described as highly metal resistant via mechanisms such as multiple and/or more efficient active resistance systems than are present in neutrophiles. However, this is not the case for all acidophiles and we contend that their growth in high metal concentrations is partially due to an intrinsic tolerance as a consequence of the environment in which they live. In this perspective, we highlight metal tolerance via complexation of free metals by sulfate ions and passive tolerance to metal influx via an internal positive cytoplasmic transmembrane potential. These tolerance mechanisms have been largely ignored in past studies of acidophile growth in the presence of metals and should be taken into account.

  • 17.
    Dopson, Mark
    et al.
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Sundkvist, J-E
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Lindström, Börje
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Toxicity of metal extraction and flotation chemicals to Sulfolobus metallicus and chalcopyrite bioleaching.2006In: Hydrometallurgy, no 81, p. 205-213Article in journal (Refereed)
  • 18. Gahan, CS
    et al.
    Sundkvist, JE
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Sandström, A
    Effect of chloride on ferrous iron oxidation by a leptospirillum ferriphilum-dominated chemostat culture2010In: Biotechnology and Bioengineering, ISSN 0006-3592, E-ISSN 1097-0290, Vol. 106, no 3, p. 422-431Article in journal (Refereed)
    Abstract [en]

    Biomining is the use of microorganisms to catalyze metal extraction from sulfide ores. However, the available water in some biomining environments has high chloride concentrations and therefore, chloride toxicity to ferrous oxidizing microorganisms has been investigated. Batch biooxidation of Fe2+ by a Leptospirillum ferriphilum dominated culture was completely inhibited by 12gL(-1) chloride. In addition, the effects of chloride on oxidation kinetics in a Fe2+ limited chemostat were studied. Results from the chemostat modeling suggest that the chloride toxicity was attributed to affects on the Fe2+ oxidation system, pH homeostasis, and lowering of the proton motive force. Modeling showed a decrease in the maximum specific growth rate (mu(max)) and an increase in the substrate constant (K-s) with increasing chloride concentrations, indicating an effect on the Fe2+ oxidation system. The model proposes a lowered maintenance activity when the media was fed with 2-3 g L-1 chloride with a concomitant drastic decrease in the true yield (Y-true). This model helps to understand the influence of chloride on Fe2+ biooxidation kinetics. Biotechnol. Bioeng. 2010;106: 422-431. (C) 2010 Wiley Periodicals, Inc.

  • 19. Kaksonen, Anna H.
    et al.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Karnachuk, Olia
    Tuovinen, Olli H.
    Puhakka, Jaakko A.
    Biological iron oxidation and sulfate reduction in the treatment of acid mine drainage at low temperatures2008In: Psychrophiles: from biodiversity to biotechnology / [ed] Rosa Margesin, Franz Schinner, Jean-Claude Marx, Charles Gerday, Berlin, Heidelberg: Springer-Verlag , 2008, p. 429-454Chapter in book (Other academic)
  • 20. Khoshkhoo, Mohammad
    et al.
    Dopson, Mark
    Shchukarev, Andrey
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sandström, Åke
    Chalcopyrite leaching and bioleaching: An X-ray photoelectron spectroscopic (XPS) investigation on the nature of hindered dissolution2014In: Hydrometallurgy, ISSN 0304-386X, E-ISSN 1879-1158, Vol. 149, p. 220-227Article in journal (Refereed)
    Abstract [en]

    Abstract Chalcopyrite (CuFeS2) is both the most economically important and the most difficult copper mineral to (bio)leach. The main reason for the slow rate of chalcopyrite dissolution is the formation of a layer on the surface of the mineral that hinders dissolution, termed “passivation”. The nature of this layer is still under debate. In this work, the role of bacterial activity was examined on the leaching efficiency of chalcopyrite by mimicking the redox potential conditions during moderately thermophilic bioleaching of a pure chalcopyrite concentrate in an abiotic experiment using chemical/electrochemical methods. The results showed that the copper recoveries were equal in the presence and absence of the mixed culture. It was found that the presence of bulk jarosite and elemental sulphur in the abiotic experiment did not hamper the copper dissolution compared to the bioleaching experiment. The leaching curves had no sign of passivation, rather that they indicated a hindered dissolution. XPS measurements carried out on massive chalcopyrite samples leached in the bioleaching and abiotic experiments revealed that common phases on the surface of the samples leached for different durations of time were elemental sulphur and iron-oxyhydroxides. The elemental sulphur on the surface of the samples was rigidly bound in a way that it did not sublimate in the ultra-high vacuum environment of the XPS spectrometer at room temperature. Jarosite was observed in only one sample from the abiotic experiment but no correlation between its presence and the hindered leaching behaviour could be made. In conclusion, a multi-component surface layer consisting of mainly elemental sulphur and iron-oxyhydroxides was considered to be responsible for the hindered dissolution.

  • 21. Kupka, Daniel
    et al.
    Liljeqvist, Maria
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Nurmi, Pauliina
    Puhakka, Jaakko A
    Tuovinen, Olli H
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Oxidation of elemental sulfur, tetrathionate and ferrous iron by the psychrotolerant Acidithiobacillus strain SS3.2009In: Research in Microbiology, ISSN 0923-2508, E-ISSN 1769-7123, Vol. 160, no 10, p. 767-74Article in journal (Refereed)
    Abstract [en]

    Mesophilic iron and sulfur-oxidizing acidophiles are readily found in acid mine drainage sites and bioleaching operations, but relatively little is known about their activities at suboptimal temperatures and in cold environments. The purpose of this work was to characterize the oxidation of elemental sulfur (S(0)), tetrathionate (S4O6(2-)) and ferrous iron (Fe2+) by the psychrotolerant Acidithiobacillus strain SS3. The rates of elemental sulfur and tetrathionate oxidation had temperature optima of 20 degrees and 25 degrees C, respectively, determined using a temperature gradient incubator that involved narrow (1.1 degrees C) incremental increases from 5 degrees to 30 degrees C. Activation energies calculated from the Arrhenius plots were 61 and 89 kJ mol(-1) for tetrathionate and 110 kJ mol(-1) for S(0) oxidation. The oxidation of elemental sulfur produced sulfuric acid at 5 degrees C and decreased the pH to approximately 1. The low pH inhibited further oxidation of the substrate. In media with both S(0) and Fe2+, oxidation of elemental sulfur did not commence until all available ferrous iron was oxidized. These data on sequential oxidation of the two substrates are in keeping with upregulation and downregulation of several proteins previously noted in the literature. Ferric iron was reduced to Fe2+ in parallel with elemental sulfur oxidation, indicating the presence of a sulfur:ferric iron reductase system in this bacterium.

  • 22.
    Kupka, Daniel
    et al.
    Institute of Geotechnics, Slovak Academy of Sciences, Watsonova 45, SK-043 53 Koice, Slovakia.
    Rzhepishevska, Olena
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Lindström, Börje
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Karnachuk, Olia V
    3Department of Agriculture and Environmental Science, Tomsk State University, Prospekt Lenina 36, 634050 Tomsk, Russia.
    Tuovinen, Olli H
    Department of Microbiology, Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210.
    Bacterial oxidation of ferrous iron at low temperatures.2007In: Biotechnology and Bioengineering, ISSN 0006-3592, E-ISSN 1097-0290, Vol. 97, no 6, p. 1470-1478Article in journal (Refereed)
    Abstract [en]

    This study comprises the first report of ferrous iron oxidation by psychrotolerant, acidophilic iron-oxidizing bacteria capable of growing at 5 degrees C. Samples of mine drainage-impacted surface soils and sediments from the Norilsk mining region (Taimyr, Siberia) and Kristineberg (Skellefte district, Sweden) were inoculated into acidic ferrous sulfate media and incubated at 5 degrees C. Iron oxidation was preceded by an approximately 3-month lag period that was reduced in subsequent cultures. Three enrichment cultures were chosen for further work and one culture designated as isolate SS3 was purified by colony isolation from a Norilsk enrichment culture for determining the kinetics of iron oxidation. The 16S rRNA based phylogeny of SS3 and two other psychrotolerant cultures, SS5 from Norilsk and SK5 from Northern Sweden, was determined. Comparative analysis of amplified 16S rRNA gene sequences showed that the psychrotolerant cultures aligned within Acidithiobacillus ferrooxidans. The rate constant of iron oxidation by growing cultures of SS3 was in the range of 0.0162-0.0104 h(-1) depending on the initial pH. The oxidation kinetics followed an exponential pattern, consistent with a first order rate expression. Parallel iron oxidation by a mesophilic reference culture of Acidithiobacillus ferrooxidans was extremely slow and linear. Precipitates harvested from the 5 degrees C culture were identified by X-ray diffraction as mixtures of schwertmannite (ideal formula Fe(8)O(8)(OH)(6)SO(4)) and jarosite (KFe(3)(SO(4))(2)(OH)(6)). Jarosite was much more dominant in precipitates produced at 30 degrees C. (c) 2007 Wiley Periodicals, Inc.

  • 23.
    Liljeqvist, Maria
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Ossandon, Francisco J.
    Gonzalez, Carolina
    Rajan, Sukithar
    Stell, Adam
    Valdes, Jorge
    Holmes, David S.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream2015In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 91, no 4, article id fiv011Article in journal (Refereed)
    Abstract [en]

    An acid mine drainage (pH 2.5-2.7) stream biofilm situated 250 m below ground in the low-temperature (6-10 degrees C) Kristineberg mine, northern Sweden, contained a microbial community equipped for growth at low temperature and acidic pH. Metagenomic sequencing of the biofilm and planktonic fractions identified the most abundant microorganism to be similar to the psychrotolerant acidophile, Acidithiobacillus ferrivorans. In addition, metagenome contigs were most similar to other Acidithiobacillus species, an Acidobacteria-like species, and a Gallionellaceae-like species. Analyses of the metagenomes indicated functional characteristics previously characterized as related to growth at low temperature including cold-shock proteins, several pathways for the production of compatible solutes and an anti-freeze protein. In addition, genes were predicted to encode functions related to pH homeostasis and metal resistance related to growth in the acidic metal-containing mine water. Metagenome analyses identified microorganisms capable of nitrogen fixation and exhibiting a primarily autotrophic lifestyle driven by the oxidation of the ferrous iron and inorganic sulfur compounds contained in the sulfidic mine waters. The study identified a low diversity of abundant microorganisms adapted to a low-temperature acidic environment as well as identifying some of the strategies the microorganisms employ to grow in this extreme environment.

  • 24.
    Liljeqvist, Maria
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Ossandon, Francisco J.
    Gonzalez, Carolina
    Rajan, Sukithar
    Stell, Adam
    Valdes, Jorge
    Holmes, David S.
    Dopson, Mark
    Metagenomic analysis reveals adaptations to a psychrotrophic lifestyle in a low temperature acid mine drainage streamManuscript (preprint) (Other academic)
  • 25.
    Liljeqvist, Maria
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Rzhepishevska, Olena I
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Gene Identification and Substrate Regulation Provide Insights into Sulfur Accumulation during Bioleaching with the Psychrotolerant Acidophile Acidithiobacillus ferrivorans2013In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 79, no 3, p. 951-957Article in journal (Refereed)
    Abstract [en]

    The psychrotolerant acidophile Acidithiobacillus ferrivorans has been identified from cold environments and has been shown to use ferrous iron and inorganic sulfur compounds as its energy sources. A bioinformatic evaluation presented in this study suggested that Acidithiobacillus ferrivorans utilized a ferrous iron oxidation pathway similar to that of the related species Acidithiobacillus ferrooxidans. However, the inorganic sulfur oxidation pathway was less clear, since the Acidithiobacillus ferrivorans genome contained genes from both Acidithiobacillus ferrooxidans and Acidithiobacillus caldus encoding enzymes whose assigned functions are redundant. Transcriptional analysis revealed that the petA1 and petB1 genes (implicated in ferrous iron oxidation) were downregulated upon growth on the inorganic sulfur compound tetrathionate but were on average 10.5-fold upregulated in the presence of ferrous iron. In contrast, expression of cyoB1 (involved in inorganic sulfur compound oxidation) was decreased 6.6-fold upon growth on ferrous iron alone. Competition assays between ferrous iron and tetrathionate with Acidithiobacillus ferrivorans SS3 precultured on chalcopyrite mineral showed a preference for ferrous iron oxidation over tetrathionate oxidation. Also, pure and mixed cultures of psychrotolerant acidophiles were utilized for the bioleaching of metal sulfide minerals in stirred tank reactors at 5 and 25°C in order to investigate the fate of ferrous iron and inorganic sulfur compounds. Solid sulfur accumulated in bioleaching cultures growing on a chalcopyrite concentrate. Sulfur accumulation halted mineral solubilization, but sulfur was oxidized after metal release had ceased. The data indicated that ferrous iron was preferentially oxidized during growth on chalcopyrite, a finding with important implications for biomining in cold environments.

  • 26.
    Liljeqvist, Maria
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Rzhepishevska, Olena I.
    Dopson, Mark
    Gene identification and substrate regulation provides insights into sulfur accumulation during bioleaching with the psychrotolerant Acidithiobacillus ferrivoransManuscript (preprint) (Other academic)
  • 27.
    Liljeqvist, Maria
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Sundkvist, Jan-Eric
    Saleh, Amang
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Low temperature removal of inorganic sulfur compounds from mining process waters2011In: Biotechnology and Bioengineering, ISSN 0006-3592, E-ISSN 1097-0290, Vol. 108, no 6, p. 1251-1259Article in journal (Refereed)
    Abstract [en]

    Process water and effluents from mining operations treating sulfide rich ores often contain considerable concentrations of metastable inorganic sulfur compounds such as thiosulfate and tetrathionate. These species may cause environmental problems if released to downstream recipients due to oxidation to sulfuric acid catalyzed by acidophilic microorganisms. Molecular phylogenic analysis of the tailings pond and recipient streams identified psychrotolerant and mesophilic inorganic sulfur compound oxidizing microorganisms. This suggested year round thiosalt oxidation occurs. Mining process waters may also contain inhibiting substances such as thiocyanate from cyanidation plants. However, toxicity experiments suggested their expected concentrations would not inhibit thiosalt oxidation by Acidithiobacillus ferrivorans SS3. A mixed culture from a permanently cold (4-6°C) low pH environment was tested for thiosalt removal in a reactor design including a biogenerator and a main reactor containing a biofilm carrier. The biogenerator and main reactors were successively reduced in temperature to 5-6°C when 43.8% of the chemical oxidation demand was removed. However, it was found that the oxidation of thiosulfate was not fully completed to sulfate since low residual concentrations of tetrathionate and trithionate were found in the discharge. This study has demonstrated the potential of using biotechnological solutions to remove inorganic sulfur compounds at 6°C and thus, reduce the impact of mining on the environment. Biotechnol. Bioeng. 2011; 108:1251-1259. © 2011 Wiley Periodicals, Inc.

  • 28.
    Liljeqvist, Maria
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Valdes, Jorge
    Holmes, David S
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Draft genome of the psychrotolerant acidophile Acidithiobacillus ferrivorans SS32011In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 193, no 16, p. 4304-4305Article in journal (Refereed)
    Abstract [en]

    Acidithiobacillus ferrivorans SS3 is a psychrotolerant acidophile capable of growth in the range of 5° to 30°C (optimum, ≈25°C). It gains energy from the oxidation of ferrous iron and inorganic sulfur compounds and obtains organic carbon from carbon dioxide. Here, we present the draft genome sequence of A. ferrivorans SS3 that will permit investigation of genes involved in growth in acidic environments at low temperatures.

  • 29. Mangold, Stefanie
    et al.
    Jonna, Venkateswara Rao
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Dopson, Mark
    Response of Acidithiobacillus caldus toward suboptimal pH conditions2013In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 17, no 4, p. 689-696Article in journal (Refereed)
    Abstract [en]

    Maintenance of a circumneutral intracellular pH is important for any organism. Acidophilic microorganisms thrive at low pH while maintaining their intracellular pH around 6.5. However, the mechanisms contributing to acidophile pH homeostasis are not well characterized. The authors investigated the proteomic response and cytoplasmic membrane fatty acid profiles of Acidithiobacillus caldus toward three pH values: 1.1, 2.5, and 4.0. Major rearrangements were observed but lower pH elicited larger changes. Differentially expressed transcription factors suggested tight transcriptional control of pH induced genes. Enzymes involved in sulfur metabolism were up-regulated at pH 1.1 suggesting either that: (1) cells required more energy for maintenance or (2) increased metabolic activity was a specific acid stress response to export intracellular protons via 1A degrees electron transport proton pumps. Furthermore, glutamate decarboxylase, an important enzyme in Escherichia coli acid resistance, was uniquely expressed at pH 1.1. Other proteins previously shown to be involved in neutrophilic acid response, such as spermidine synthase, PspA, and toluene tolerance protein, were differentially expressed in At. caldus but require further investigation to show a direct link to pH homeostasis. Their roles in acidophilic organisms are discussed. Active modulation of fatty acid profiles was detected and suggested a more rigid membrane at low pH.

  • 30.
    Mangold, Stefanie
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Potrykus, Joanna
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Aberdeen Fungal Group, University of Aberdeen, Scotland, UK.
    Björn, Erik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lövgren, Lars
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Centre for Ecology and Evolution in Microbial Model Systems, School of Natural Sciences, Linnaeus University, Kalmar, Sweden.
    Extreme zinc tolerance in acidophilic microorganisms from the bacterial and archaeal domains2013In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 17, no 1, p. 75-85Article in journal (Refereed)
    Abstract [en]

    Zinc can occur in extremely high concentrations in acidic, heavy metal polluted environments inhabited by acidophilic prokaryotes. Although these organisms are able to thrive in such severely contaminated ecosystems their resistance mechanisms have not been well studied. Bioinformatic analysis of a range of acidophilic bacterial and archaeal genomes identified homologues of several known zinc homeostasis systems. These included primary and secondary transporters, such as the primary heavy metal exporter ZntA and Nramp super-family secondary importer MntH. Three acidophilic model microorganisms, the archaeon 'Ferroplasma acidarmanus', the Gram negative bacterium Acidithiobacillus caldus, and the Gram positive bacterium Acidimicrobium ferrooxidans, were selected for detailed analyses. Zinc speciation modeling of the growth media demonstrated that a large fraction of the free metal ion is complexed, potentially affecting its toxicity. Indeed, many of the putative zinc homeostasis genes were constitutively expressed and with the exception of 'F. acidarmanus' ZntA, they were not up-regulated in the presence of excess zinc. Proteomic analysis revealed that zinc played a role in oxidative stress in At. caldus and Am. ferrooxidans. Furthermore, 'F. acidarmanus' kept a constant level of intracellular zinc over all conditions tested whereas the intracellular levels increased with increasing zinc exposure in the remaining organisms.

  • 31.
    Mangold, Stefanie
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    rao Jonna, Venkateswara
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Response of Acidithiobacillus caldus towards suboptimal pH conditionsManuscript (preprint) (Other academic)
  • 32.
    Mangold, Stefanie
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Valdés, Jorge
    Holmes, David S
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Sulfur metabolism in the extreme acidophile acidithiobacillus caldus2011In: Frontiers in microbiology, ISSN 1664-302X, Vol. 2, p. 17-Article in journal (Refereed)
    Abstract [en]

    Given the challenges to life at low pH, an analysis of inorganic sulfur compound (ISC) oxidation was initiated in the chemolithoautotrophic extremophile Acidithiobacillus caldus. A. caldus is able to metabolize elemental sulfur and a broad range of ISCs. It has been implicated in the production of environmentally damaging acidic solutions as well as participating in industrial bioleaching operations where it forms part of microbial consortia used for the recovery of metal ions. Based upon the recently published A. caldus type strain genome sequence, a bioinformatic reconstruction of elemental sulfur and ISC metabolism predicted genes included: sulfide-quinone reductase (sqr), tetrathionate hydrolase (tth), two sox gene clusters potentially involved in thiosulfate oxidation (soxABXYZ), sulfur oxygenase reductase (sor), and various electron transport components. RNA transcript profiles by semi quantitative reverse transcription PCR suggested up-regulation of sox genes in the presence of tetrathionate. Extensive gel based proteomic comparisons of total soluble and membrane enriched protein fractions during growth on elemental sulfur and tetrathionate identified differential protein levels from the two Sox clusters as well as several chaperone and stress proteins up-regulated in the presence of elemental sulfur. Proteomics results also suggested the involvement of heterodisulfide reductase (HdrABC) in A. caldus ISC metabolism. A putative new function of Hdr in acidophiles is discussed. Additional proteomic analysis evaluated protein expression differences between cells grown attached to solid, elemental sulfur versus planktonic cells. This study has provided insights into sulfur metabolism of this acidophilic chemolithotroph and gene expression during attachment to solid elemental sulfur.

  • 33. Morales, Teresita A
    et al.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Athar, Rana
    Herbert, Roger B
    Analysis of bacterial diversity in acidic pond water and compost after treatment of artificial acid mine drainage for metal removal.2005In: Biotechnol Bioeng, ISSN 0006-3592, Vol. 90, no 5, p. 543-51Article in journal (Refereed)
    Abstract [en]

    The microbial population of a sludge amended leaf compost material utilized for treatment of artificial acid mine drainage was studied by culture-independent molecular methods. Iron-rich and sulfurous wastewater (artificial acid mine drainage) was circulated through a column bioreactor for 16 months. After 12 months the column was inoculated with a mixed culture from an acidic pond receiving acid mine drainage from a tailings impoundment at a decommissioned site in Kristineberg, North Sweden. Hydrogen sulfide odor and the formation of black precipitates indicated that sulfate-reduction occurred in the column. 16S rDNA gene analysis by denaturing gradient gel electrophoresis, cloning, and sequencing as well as fluorescent in situ hybridization confirmed the presence of microorganisms closely related to sulfate-reducing bacteria and microorganisms from the genera Pseudoxanthmonas, Dechlorosoma, Desulfovibrio, Agrobacterium, Methylocapsa, Rhodococcus, Sulfobacillus, and some unidentified bacteria. Sulfate-reducing bacteria were found in the column bioreactor 2 weeks after inoculation, but not thereafter. This suggests they were in low abundance, even though sulfate remediation rates were significant. Instead, the population contained species similar to those previously found to utilize humic substances released from the compost material. (c) 2005 Wiley Periodicals, Inc.

  • 34. Nicomrat, D
    et al.
    Dick, WA
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Tuovinen, OH
    Bacterial phylogenetic diversity in a constructed wetland system treating acid coal mine drainage.2008In: Soil Biol Biochem, Vol. 40, p. 312-321Article in journal (Refereed)
  • 35.
    Osorio, Hector
    et al.
    Center for Bioinformatics and Genome Biology, Fundacion Ciencia y Vida, Santiago and Depto. Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile.
    Mangold, Stefanie
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Denis, Yann
    CNRS and Aix-Marseille Université, IMM, Plateforme Transcriptome, 13009 Marseille, France.
    Nancucheo, Ivan
    College of Natural Sciences, Bangor University, Bangor LL57 2UW, U.K..
    Johnson, D. Barrie
    College of Natural Sciences, Bangor University, Bangor LL57 2UW, U.K.
    Bonnefoy, Violaine
    CNRS and Aix-Marseille Université, IMM, Laboratoire de Chimie Bactérienne UMR7283, 13009 Marseille, France.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Holmes, David S.
    Center for Bioinformatics and Genome Biology, Fundacion Ciencia y Vida, Santiago and Depto. Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile.
    Anaerobic Sulfur Metabolism Coupled to Dissimilatory Iron Reduction in the Extremophile Acidithiobacillus ferrooxidans2013In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 79, no 7, p. 2172-2181Article in journal (Refereed)
    Abstract [en]

    Gene transcription (microarrays) and protein levels (proteomics) were compared in cultures of the acidophilic chemolithotroph Acidithiobacillus ferrooxidans grown on elemental sulfur as the electron donor under aerobic and anaerobic conditions, using either molecular oxygen or ferric iron as the electron acceptor, respectively. No evidence supporting the role of either tetrathionate hydrolase or arsenic reductase in mediating the transfer of electrons to ferric iron (as suggested by previous studies) was obtained. In addition, no novel ferric iron reductase was identified. However, data suggested that sulfur was disproportionated under anaerobic conditions, forming hydrogen sulfide via sulfur reductase and sulfate via heterodisulfide reductase and ATP sulfurylase. Supporting physiological evidence for H2S production came from the observation that soluble Cu2+ included in anaerobically incubated cultures was precipitated (seemingly as CuS). Since H2S reduces ferric iron to ferrous in acidic medium, its production under anaerobic conditions indicates that anaerobic iron reduction is mediated, at least in part, by an indirect mechanism. Evidence was obtained for an alternative model implicating the transfer of electrons from S-0 to Fe3+ via a respiratory chain that includes a bc(1) complex and a cytochrome c. Central carbon pathways were upregulated under aerobic conditions, correlating with higher growth rates, while many Calvin-Benson-Bassham cycle components were upregulated during anaerobic growth, probably as a result of more limited access to carbon dioxide. These results are important for understanding the role of A. ferrooxidans in environmental biogeochemical metal cycling and in industrial bioleaching operations.

  • 36. Potrykus, Joanna
    et al.
    Jonna, Venkateswara Rao
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Iron homeostasis and responses to iron limitation in extreme acidophiles from the Ferroplasma genus2011In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 11, no 1, p. 52-63Article in journal (Refereed)
    Abstract [en]

    Extremely acidophilic archaea from the genus Ferroplasma inhabit iron-rich biomining environments and are important constituents of naturally occurring microbial consortia that catalyze the production of acid mine drainage. A combined bioinformatic, transcript profiling, and proteomic approach was used to elucidate iron homeostasis mechanisms in "F. acidarmanus" Fer1 and F. acidiphilum Y(T) . Bioinformatic analysis of the "F. acidarmanus" Fer1 genome sequence revealed genes encoding proteins hypothesized to be involved in iron-dependent gene regulation and siderophore biosynthesis; the Fhu and NRAMP cation acquisition systems; iron storage proteins; and the SUF machinery for the biogenesis of Fe-S clusters. A subset of homologous genes was identified on the F. acidiphilum Y(T) chromosome by direct PCR probing. In both strains, some of the genes appeared to be regulated in a ferrous/ferric iron-dependent manner, as indicated by RT-PCR. A detailed gel-based proteomics analysis of responses to iron depletion showed that a putative isochorismatase, presumably involved in siderophore biosynthesis, and the SufBCD system were upregulated under iron-limiting conditions. No evidence was obtained for iron sparing response during iron limitation. This study constitutes the first detailed investigation of iron homeostasis in extremely acidophilic archaea.

  • 37.
    Rzhepishevska, Olena I.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Dopson, Mark
    Sulphur Accumulation During Low Temperature BioleachingManuscript (preprint) (Other (popular science, discussion, etc.))
  • 38.
    Rzhepishevska, Olena I
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Valdés, Jorge
    Center for Bioinformatics and Genome Biology, Life Science Foundation, MIFAB and Andrés Bello University, Santiago, Chile.
    Marcinkeviciene, Liucija
    Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Mokslininku 12, Vilnius LT-08662, Lithuania.
    Gallardo, Camelia Algora
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Meskys, Rolandas
    Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Mokslininku 12, Vilnius LT-08662, Lithuania.
    Bonnefoy, Violaine
    CNRS, IBSM, Laboratoire de Chimie Bactérienne, 31 Chemin J. Aiguier, 13402 Marseille Cedex 20, France.
    Holmes, David S.
    Center for Bioinformatics and Genome Biology, Life Science Foundation, MIFAB and Andrés Bello University, Santiago, Chile.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Regulation of a novel Acidithiobacillus caldus gene cluster involved in metabolism of reduced inorganic sulfur compounds2007In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 73, no 22, p. 7367-7372Article in journal (Refereed)
    Abstract [en]

    Acidithiobacillus caldus has been proposed to play a role in the oxidation of reduced inorganic sulfur compounds (RISCs) produced in industrial biomining of sulfidic minerals. Here, we describe the regulation of a new cluster containing the gene encoding tetrathionate hydrolase (tetH), a key enzyme in the RISC metabolism of this bacterium. The cluster contains five cotranscribed genes, ISac1, rsrR, rsrS, tetH, and doxD, coding for a transposase, a two-component response regulator (RsrR and RsrS), tetrathionate hydrolase, and DoxD, respectively. As shown by quantitative PCR, rsrR, tetH, and doxD are upregulated to different degrees in the presence of tetrathionate. Western blot analysis also indicates upregulation of TetH in the presence of tetrathionate, thiosulfate, and pyrite. The tetH cluster is predicted to have two promoters, both of which are functional in Escherichia coli and one of which was mapped by primer extension. A pyrrolo-quinoline quinone binding domain in TetH was predicted by bioinformatic analysis, and the presence of an o-quinone moiety was experimentally verified, suggesting a mechanism for tetrathionate oxidation.

  • 39.
    Rzhepishevska, Olena
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Lindström, Börje
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Tuovinen, Olli H
    Department of Microbiology, Ohio State University, 484 W 12th Avenue, Columbus, Ohio 43210.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Bioleaching of sulfidic tailing samples with a novel, vacuum-positive pressure driven bioreactor.2005In: Biotechnology and Bioengineering, ISSN 0006-3592, E-ISSN 1097-0290, Vol. 92, no 5, p. 559-67Article in journal (Refereed)
    Abstract [en]

    This study presents a design for a novel bioreactor that uses alternating vacuum and positive pressure cycles to transfer acidic leach solution in and out of contact with finely ground sulfidic mine tailings. These tailings constitute an environmental problem that needs experimental data to support the development of management and control strategies. A conventional stirred tank bioreactor was used as a reference system. Both bioreactors were inoculated with mixed cultures of acidophilic iron and sulfur oxidizers. The rate of the bioleaching of tailings was 0.50 +/- 0.14 g Fe/L . day in the stirred tank bioreactor and 0.17 +/- 0.05 g Fe/L . day in the novel bioreactor. Microbial populations were identified in the two-bioreactor systems by analysis of 16S rRNA genes involving amplification, denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. The inoculum contained sulfur-oxidizing Acidithiobacillus caldus and Acidithiobacillus thiooxidans, iron oxidizers from the genera Leptospirillum and Ferroplasma, and a chemoorganotrophic Alicyclobacillus sp. During bioleaching of the tailings, the microbial populations in both bioreactors were similar to the inoculum culture, except that At. thiooxidans outgrew At. caldus. Sequences consistent with a Sulfobacillus sp. were amplified from both bioreactor samples although this bacterium was initially below the level of detection in the inoculum. After prolonged operation, Ferroplasma acidiphilum and an uncultured bacterium related to the CFB group were also detected in the novel bioreactor, whereas Sulfobacillus sp. was no longer detected. The novel bioreactor has potential uses in other areas of environmental biotechnology that involves periodic contact of liquids with solid substrates. (c) 2005 Wiley Periodicals, Inc.

  • 40.
    Slonczewski, Joan L.
    et al.
    Department of Biology, Kenyon College.
    Fujisawa, Makoto
    Mt Sinai Sch Med, Dept Pharmacol & Syst Therapeut, New York, NY USA.
    Dopson, Mark
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Krulwich, Terry A.
    Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine.
    Cytoplasmic pH Measurement and Homeostasis in Bacteria and Archaea2009In: Advances in Microbial Physiology, Vol 55 / [ed] Robert K. Poole, University of Sheffield, UK, Academic Press, 2009, p. 1-79Chapter in book (Refereed)
    Abstract [en]

    Of all the molecular determinants for growth, the hydronium and hydroxide ions are found naturally in the widest concentration range, from acid mine drainage below pH 0 to soda lakes above pH 13. Most bacteria and archaea have mechanisms that maintain their internal, cytoplasmic pH within a narrower range than the pH outside the cell, termed "pH homeostasis." Some mechanisms of pH homeostasis are specific to particular species or groups of microorganisms while some common principles apply across the pH spectrum. The measurement of internal pH of microbes presents challenges, which are addressed by a range of techniques under varying growth conditions. This review compares and contrasts cytoplasmic pH homeostasis in acidophilic, neutralophilic, and alkaliphilic bacteria and archaea under conditions of growth, non-growth survival, and biofilms. We present diverse mechanisms of pH homeostasis including cell buffering, adaptations of membrane structure, active ion transport, and metabolic consumption of acids and bases.

  • 41. Zammit, Carla M.
    et al.
    Mangold, Stefanie
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Jonna, Venkateswara Rao
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Mutch, Lesley A.
    Watling, Helen R.
    Dopson, Mark
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Watkin, Elizabeth L. J.
    Bioleaching in brackish waters-effect of chloride ions on the acidophile population and proteomes of model species2012In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 93, no 1, p. 319-329Article in journal (Refereed)
    Abstract [en]

    High concentrations of chloride ions inhibit the growth of acidophilic microorganisms used in biomining, a problem particularly relevant to Western Australian and Chilean biomining operations. Despite this, little is known about the mechanisms acidophiles adopt in order to tolerate high chloride ion concentrations. This study aimed to investigate the impact of increasing concentrations of chloride ions on the population dynamics of a mixed culture during pyrite bioleaching and apply proteomics to elucidate how two species from this mixed culture alter their proteomes under chloride stress. A mixture consisting of well-known biomining microorganisms and an enrichment culture obtained from an acidic saline drain were tested for their ability to bioleach pyrite in the presence of 0, 3.5, 7, and 20 g L(-1) NaCl. Microorganisms from the enrichment culture were found to out-compete the known biomining microorganisms, independent of the chloride ion concentration. The proteomes of the Gram-positive acidophile Acidimicrobium ferrooxidans and the Gram-negative acidophile Acidithiobacillus caldus grown in the presence or absence of chloride ions were investigated. Analysis of differential expression showed that acidophilic microorganisms adopted several changes in their proteomes in the presence of chloride ions, suggesting the following strategies to combat the NaCl stress: adaptation of the cell membrane, the accumulation of amino acids possibly as a form of osmoprotectant, and the expression of a YceI family protein involved in acid and osmotic-related stress.

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