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Dopson, Mark
Publications (10 of 41) Show all publications
Liljeqvist, M., Ossandon, F. J., Gonzalez, C., Rajan, S., Stell, A., Valdes, J., . . . Dopson, M. (2015). Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream. FEMS Microbiology Ecology, 91(4), Article ID fiv011.
Open this publication in new window or tab >>Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream
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2015 (English)In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 91, no 4, article id fiv011Article in journal (Refereed) Published
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.

Keywords
metagenome, acid mine drainage, psychrotolerant, Acidithiobacillus ferrivorans, low temperature
National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-106514 (URN)10.1093/femsec/fiv011 (DOI)000355327300002 ()
Available from: 2015-07-15 Created: 2015-07-14 Last updated: 2018-06-07Bibliographically approved
Khoshkhoo, M., Dopson, M., Shchukarev, A. & Sandström, Å. (2014). Chalcopyrite leaching and bioleaching: An X-ray photoelectron spectroscopic (XPS) investigation on the nature of hindered dissolution. Hydrometallurgy, 149, 220-227
Open this publication in new window or tab >>Chalcopyrite leaching and bioleaching: An X-ray photoelectron spectroscopic (XPS) investigation on the nature of hindered dissolution
2014 (English)In: Hydrometallurgy, ISSN 0304-386X, E-ISSN 1879-1158, Vol. 149, p. 220-227Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Elsevier, 2014
Keywords
Chalcopyrite, Bioleaching, Passivation, Redox potential, XPS
National Category
Chemical Sciences
Identifiers
urn:nbn:se:umu:diva-93708 (URN)10.1016/j.hydromet.2014.08.012 (DOI)000344204400026 ()
Available from: 2014-09-30 Created: 2014-09-30 Last updated: 2018-06-07Bibliographically approved
Dopson, M., Ossandon, F. J., Lövgren, L. & Holmes, D. S. (2014). Metal resistance or tolerance?: Acidophiles confront high metal loads via both abiotic and biotic mechanisms. Frontiers in Microbiology, 5, 157
Open this publication in new window or tab >>Metal resistance or tolerance?: Acidophiles confront high metal loads via both abiotic and biotic mechanisms
2014 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 5, p. 157-Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Frontiers Media, 2014
Keywords
metal, acidophile, resistance, tolerance, homeostasis, biomining
National Category
Chemical Sciences Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:umu:diva-88950 (URN)10.3389/fmicb.2014.00157 (DOI)000334278500001 ()
Available from: 2014-05-22 Created: 2014-05-19 Last updated: 2018-06-07Bibliographically approved
Osorio, H., Mangold, S., Denis, Y., Nancucheo, I., Johnson, D. B., Bonnefoy, V., . . . Holmes, D. S. (2013). Anaerobic Sulfur Metabolism Coupled to Dissimilatory Iron Reduction in the Extremophile Acidithiobacillus ferrooxidans. Applied and Environmental Microbiology, 79(7), 2172-2181
Open this publication in new window or tab >>Anaerobic Sulfur Metabolism Coupled to Dissimilatory Iron Reduction in the Extremophile Acidithiobacillus ferrooxidans
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2013 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 79, no 7, p. 2172-2181Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
American Society for Microbiology, 2013
National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-60633 (URN)10.1128/AEM.03057-12 (DOI)000316183500008 ()
Note

Originally published in thesis in manuscript form

Available from: 2012-10-22 Created: 2012-10-22 Last updated: 2018-06-08Bibliographically approved
Mangold, S., Potrykus, J., Björn, E., Lövgren, L. & Dopson, M. (2013). Extreme zinc tolerance in acidophilic microorganisms from the bacterial and archaeal domains. Extremophiles, 17(1), 75-85
Open this publication in new window or tab >>Extreme zinc tolerance in acidophilic microorganisms from the bacterial and archaeal domains
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2013 (English)In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 17, no 1, p. 75-85Article in journal (Refereed) Published
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.

Keywords
Acid mine drainage, Acidophile, Metal resistance, Modeling, Zinc
National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-60634 (URN)10.1007/s00792-012-0495-3 (DOI)000312779200007 ()23143658 (PubMedID)
Available from: 2012-10-22 Created: 2012-10-22 Last updated: 2018-06-08Bibliographically approved
Liljeqvist, M., Rzhepishevska, O. I. & Dopson, M. (2013). Gene Identification and Substrate Regulation Provide Insights into Sulfur Accumulation during Bioleaching with the Psychrotolerant Acidophile Acidithiobacillus ferrivorans. Applied and Environmental Microbiology, 79(3), 951-957
Open this publication in new window or tab >>Gene Identification and Substrate Regulation Provide Insights into Sulfur Accumulation during Bioleaching with the Psychrotolerant Acidophile Acidithiobacillus ferrivorans
2013 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 79, no 3, p. 951-957Article in journal (Refereed) Published
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.

National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-66140 (URN)10.1128/AEM.02989-12 (DOI)000313989700024 ()23183980 (PubMedID)
Available from: 2013-02-15 Created: 2013-02-15 Last updated: 2018-06-08Bibliographically approved
Mangold, S., Jonna, V. R. & Dopson, M. (2013). Response of Acidithiobacillus caldus toward suboptimal pH conditions. Extremophiles, 17(4), 689-696
Open this publication in new window or tab >>Response of Acidithiobacillus caldus toward suboptimal pH conditions
2013 (English)In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 17, no 4, p. 689-696Article in journal (Refereed) Published
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.

Keywords
Acidithiobacillus caldus, Acidophiles, pH homeostasis, Proteomics, Fatty acid methyl ester
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-79259 (URN)10.1007/s00792-013-0553-5 (DOI)000320889100014 ()
Available from: 2013-09-05 Created: 2013-08-13 Last updated: 2018-06-08Bibliographically approved
Zammit, C. M., Mangold, S., Jonna, V. R., Mutch, L. A., Watling, H. R., Dopson, M. & Watkin, E. L. J. (2012). Bioleaching in brackish waters-effect of chloride ions on the acidophile population and proteomes of model species. Applied Microbiology and Biotechnology, 93(1), 319-329
Open this publication in new window or tab >>Bioleaching in brackish waters-effect of chloride ions on the acidophile population and proteomes of model species
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2012 (English)In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 93, no 1, p. 319-329Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
New York: Springer, 2012
Keywords
Biomining, Chloride, Proteomics, Brackish, Membrane
National Category
Other Medical Biotechnology
Identifiers
urn:nbn:se:umu:diva-52179 (URN)10.1007/s00253-011-3731-3 (DOI)000298853600029 ()
Available from: 2012-02-17 Created: 2012-02-13 Last updated: 2018-06-08Bibliographically approved
Liljeqvist, M., Valdes, J., Holmes, D. S. & Dopson, M. (2011). Draft genome of the psychrotolerant acidophile Acidithiobacillus ferrivorans SS3. Journal of Bacteriology, 193(16), 4304-4305
Open this publication in new window or tab >>Draft genome of the psychrotolerant acidophile Acidithiobacillus ferrivorans SS3
2011 (English)In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 193, no 16, p. 4304-4305Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
American Society for Microbiology, 2011
National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-56530 (URN)10.1128/JB.05373-11 (DOI)21705598 (PubMedID)
Available from: 2012-06-20 Created: 2012-06-20 Last updated: 2018-06-08Bibliographically approved
Potrykus, J., Jonna, V. R. & Dopson, M. (2011). Iron homeostasis and responses to iron limitation in extreme acidophiles from the Ferroplasma genus. Proteomics, 11(1), 52-63
Open this publication in new window or tab >>Iron homeostasis and responses to iron limitation in extreme acidophiles from the Ferroplasma genus
2011 (English)In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 11, no 1, p. 52-63Article in journal (Refereed) Published
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.

Keywords
Extreme acidophile;“Ferroplasma acidarmanus” Fer1;Ferroplasma acidiphilum;Iron homeostasis;Microbiology;Peptide mass fingerprinting
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-43232 (URN)10.1002/pmic.201000193 (DOI)21182194 (PubMedID)
Available from: 2011-04-22 Created: 2011-04-22 Last updated: 2018-06-08Bibliographically approved
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