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  • 1.
    Abromaitis, V.
    et al.
    Kaunas Univ Technol, Lithuania ; Wetsus, European Ctr Excellence Sustainable Water Technol, Netherlands.
    Racys, V.
    Kaunas Univ Technol, Lithuania.
    van der Marel, P.
    WLN, Netherlands.
    Ni, Gaofeng
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wolthuizen, A. L.
    Wageningen Univ, Netherlands.
    Meulepas, R. J. W.
    Wetsus, European Ctr Excellence Sustainable Water Technol, Netherlands.
    Effect of shear stress and carbon surface roughness on bioregeneration and performance of suspended versus attached biomass in metoprolol-loaded biological activated carbon systems2017In: Chemical Engineering Journal, ISSN 1385-8947, E-ISSN 1873-3212, Vol. 317, p. 503-511Article in journal (Refereed)
    Abstract [en]

    The bioregeneration of activated carbon (AC) in biological activated carbon (BAC) systems is limited by sorption-desorption hysteresis and transport between the adsorbent and biomass. In this study, we investigated these limitations and whether a biofilm covering the AC surface is required. Consequently, BAC reactors were operated at different shear stress and AC surface smoothness, since this may affect biofilm formation. The experiments were carried out in BAC and blank reactors treating synthetic wastewater containing the pharmaceutical metoprolol. After start-up, all reactors removed metoprolol completely; however, after 840 h the removal dropped due to saturation of the AC. In the blank reactors, the removal dropped to 0% while in the BAC reactors removal recovered to >99%, due to increased biological activity. During the initial phase, the metoprolol was adsorbed, rather than biodegraded. At the end, the AC from the BAC reactors had higher pore volume and sorption capacity than from the blank reactors, showing that the AC had been bioregenerated. At high shear (G = 25 s(-1)), the rough AC granules (R-a = 13 mu m) were covered with a 50-400 gm thick biofilm and the total protein content of the biofilm was 2.6 mg/gAC, while at lower shear (G = 8.8 s(-1)) the rough AC granules were only partly covered. The biofilm formation at lower shear (G = 8.8 s(-1)) on smooth AC granules (R-a = 1.6 mu m) was negligible. However, due to the presence of suspended biomass the reactor performance or bioregeneration were not reduced. This showed that direct contact between the AC and biomass was not essential in mixed BAC systems. The microbial analyses of the suspended biomass and the biofilm on AC surface indicated that metoprolol was mainly biodegraded in suspension. (C) 2017 Elsevier B.V. All rights reserved.

  • 2.
    Acuna, Lillian G.
    et al.
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Pablo Cardenas, Juan
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Covarrubias, Paulo C.
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Jose Haristoy, Juan
    Fundación Ciencia & Vida, Chile.
    Flores, Rodrigo
    Fundación Ciencia & Vida, Chile.
    Nuñez, Harold
    Fundación Ciencia & Vida, Chile.
    Riadi, Gonzalo
    Universidad de Talca, Chile.
    Shmaryahu, Amir
    Fundación Ciencia & Vida, Chile.
    Valdes, Jorge
    Center for Systems Biotechnology, Chile.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Rawlings, Douglas E.
    University of Stellenbosch, South Africa.
    Banfield, Jillian F.
    University of California, USA.
    Holmes, David S.
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Quatrini, Raquel
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 11, article id e78237Article in journal (Refereed)
    Abstract [en]

    Background: Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. Principal Findings: Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions. Significance: For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche.

  • 3.
    Baker-Austin, Craig
    et al.
    Savannah River Ecology Laboratory, University of Georgia, USA.
    Dopson, Mark
    Umeå University.
    Life in acid: pH homeostasis in acidophiles.2007In: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 15, no 4, p. 165-171Article, review/survey (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.

  • 4.
    Baker-Austin, Craig
    et al.
    University of East Anglia, UK.
    Dopson, Mark
    University of East Anglia, UK.
    Wexler, Margaret
    University of East Anglia, UK.
    Sawers, R Gary
    John Innes Centre, Norwich, UK.
    Bond, Philip L
    University of East Anglia, UK ; .
    Molecular insight into extreme copper resistance in the extremophilic archaeon 'Ferroplasma acidarmanus' Fer1.2005In: Microbiology, ISSN 1350-0872, E-ISSN 1465-2080, Vol. 151, no 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.

  • 5.
    Baker-Austin, Craig
    et al.
    University of East Anglia, UK ; University of Georgia, USA.
    Dopson, Mark
    University of East Anglia, UK ; Umeå University.
    Wexler, Margaret
    University of East Anglia, UK.
    Sawers, R Gary
    John Innes Centre, Norwich, UK.
    Stemmler, Ann
    Wayne State University, School of Medicine, Detroit, USA.
    Rosen, Barry P
    Wayne State University, School of Medicine, Detroit, USA.
    Bond, Philip L
    University of East Anglia, UK ; University of Queensland, Brisbane, Australia.
    Extreme arsenic resistance by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.2007In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, 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.

  • 6.
    Baker-Austin, Craig
    et al.
    University of East Anglia, UK ; Cefas Weymouth Laboratory, Dorset, UK.
    Potrykus, Joanna
    Umeå University.
    Wexler, Margaret
    University of East Anglia, UK.
    Bond, Philip L
    University of East Anglia, UK ; University of Queensland, Brisbane, Australia.
    Dopson, Mark
    University of East Anglia, UK ; Umeå University.
    Biofilm development in the extremely acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.2010In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 14, no 6, p. 485-491Article in journal (Refereed)
    Abstract [en]

    'Ferroplasma acidarmanus' Fer1 is an iron-oxidizing extreme acidophile isolated from the Iron Mountain mine, California, USA. This archaeon is predominantly found in biofilm-associated structures in the environment, and produces two distinct biofilm morphologies. Bioinformatic analysis of the 'F. acidarmanus' Fer1 genome identified genes annotated as involved in attachment and biofilm formation. No putative quorum sensing signaling genes were identified and no N-acyl homoserine lactone-like compounds were found in 'F. acidarmanus' Fer1 biofilm supernatant. Scanning confocal microscopy analysis of biofilm development on the surface of pyrite demonstrated the temporal and spatial development of biofilm growth. Furthermore, two-dimensional polyacrylamide gel electrophoresis was used to examine differential protein expression patterns between biofilm and planktonic populations. Ten up-regulated proteins were identified that included six enzymes associated with anaerobic growth, suggesting that the dominating phenotype in the mature biofilm was associated with anaerobic modes of growth. This report increases our knowledge of the genetic and proteomic basis of biofilm formation in an extreme acidophilic archaeon.

  • 7.
    Bellenberg, Soren
    et al.
    Univ Duisburg Essen, Germany.
    Buetti-Dinh, Antoine
    Univ Svizzera Italiana, Switzerland;Swiss Inst Bioinformat, Switzerland.
    Galli, Vanni
    Univ Appl Sci Southern Switzerland, Switzerland.
    Ilie, Olga
    Univ Svizzera Italiana, Switzerland;Swiss Inst Bioinformat, Switzerland.
    Herold, Malte
    Univ Luxembourg, Luxembourg.
    Christel, Stephan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Boretska, Mariia
    Univ Duisburg Essen, Germany.
    Pivkin, Igor V.
    Univ Svizzera Italiana, Switzerland;Swiss Inst Bioinformat, Switzerland.
    Wilmes, Paul
    Univ Luxembourg, Luxembourg.
    Sand, Wolfgang
    Univ Duisburg Essen, Germany;Donghua Univ, Peoples Republic of China;Tech Univ Bergakad Freiberg, Germany.
    Vera, Mario
    Pontificia Univ Catolica Chile, Chile.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms2018In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 84, no 20, article id UNSP e01835-18Article in journal (Refereed)
    Abstract [en]

    Industrial biomining processes are currently focused on metal sulfides and their dissolution, which is catalyzed by acidophilic iron(II)- and/or sulfur-oxidizing microorganisms. Cell attachment on metal sulfides is important for this process. Biofilm formation is necessary for seeding and persistence of the active microbial community in industrial biomining heaps and tank reactors, and it enhances metal release. In this study, we used a method for direct quantification of the mineral-attached cell population on pyrite or chalcopyrite particles in bioleaching experiments by coupling high-throughput, automated epifluorescence microscopy imaging of mineral particles with algorithms for image analysis and cell quantification, thus avoiding human bias in cell counting. The method was validated by quantifying cell attachment on pyrite and chalcopyrite surfaces with axenic cultures of Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans. The method confirmed the high affinity of L. ferriphilum cells to colonize pyrite and chalcopyrite surfaces and indicated that biofilm dispersal occurs in mature pyrite batch cultures of this species. Deep neural networks were also applied to analyze biofilms of different microbial consortia. Recent analysis of the L. ferriphilum genome revealed the presence of a diffusible soluble factor (DSF) family quorum sensing system. The respective signal compounds are known as biofilm dispersal agents. Biofilm dispersal was confirmed to occur in batch cultures of L. ferriphilum and S. thermosulfidooxidans upon the addition of DSF family signal compounds. IMPORTANCE The presented method for the assessment of mineral colonization allows accurate relative comparisons of the microbial colonization of metal sulfide concentrate particles in a time-resolved manner. Quantitative assessment of the mineral colonization development is important for the compilation of improved mathematical models for metal sulfide dissolution. In addition, deep-learning algorithms proved that axenic or mixed cultures of the three species exhibited characteristic biofilm patterns and predicted the biofilm species composition. The method may be extended to the assessment of microbial colonization on other solid particles and may serve in the optimization of bioleaching processes in laboratory scale experiments with industrially relevant metal sulfide concentrates. Furthermore, the method was used to demonstrate that DSF quorum sensing signals directly influence colonization and dissolution of metal sulfides by mineral-oxidizing bacteria, such as L. ferriphilum and S. thermosulfidooxidans.

  • 8.
    Bijmans, Martijn F M
    et al.
    Wageningen University and Research Centre, Wageningen, The Netherlands.
    de Vries, Erik
    Wageningen University and Research Centre, Wageningen, The Netherlands.
    Yang, Chun-Hui
    Umeå University.
    N Buisman, Cees J
    Wageningen University and Research Centre, Wageningen, The Netherlands.
    Lens, Piet N L
    Wageningen University and Research Centre, Wageningen, The Netherlands.
    Dopson, Mark
    Umeå University.
    Sulfate reduction at pH 4.0 for treatment of process and wastewaters.2010In: 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.

  • 9.
    Bijmans, Martijn F M
    et al.
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Dopson, Mark
    Umeå University.
    Ennin, Frederick
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Lens, Piet N L
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Buisman, Cees J N
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    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. 1809-1818Article 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.

  • 10.
    Bijmans, Martijn F M
    et al.
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Dopson, Mark
    Umeå University.
    Peeters, Tom W T
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Lens, Piet N L
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Buisman, Cees J N
    Wageningen University and Research Centre, Wageningen,The Netherlands.
    Sulfate reduction at pH 5 in a high-rate membrane bioreactor: reactor performance and microbial community analyses.2009In: Journal of Microbiology and Biotechnology, ISSN 1017-7825, E-ISSN 1738-8872, Vol. 19, no 7, p. 698-708Article in journal (Refereed)
    Abstract [en]

    High rate sulfate reduction under acidic conditions opens possibilities for new process flow sheets that allow the selective recovery of metals from mining and metallurgical waste and process water. However, knowledge about high-rate sulfate reduction under acidic conditions is limited. This paper investigates sulfate reduction in a membrane bioreactor at a controlled pH of 5. Sulfate and formate were dosed using a pH-auxostat system while formate was converted into hydrogen, which was used for sulfate reduction. Sulfide was removed from the gas phase to prevent sulfide inhibition. This study shows a high-rate sulfate-reducing bioreactor system for the first time at pH 5, with a volumetric activity of 188mmol SO(4)(2-)/I/d and a specific activity of 81mmol SO(4)(2-) volatile suspended. The microbial community at the end of the reactor run consisted of a diverse mixed population including sulfate-reducing bacteria.

  • 11.
    Bijmans, Martijn F M
    et al.
    Univ Wageningen & Res Ctr, Wageningen, Netherlands.
    van Helvoort, Pieter-Jan
    Univ Wageningen & Res Ctr, Wageningen, Netherlands.
    Dar, Shabir A
    Umeå University.
    Dopson, Mark
    Umeå University.
    Lens, Piet N L
    Univ Wageningen & Res Ctr, Wageningen, Netherlands.
    Buisman, Cees J N
    Univ Wageningen & Res Ctr, Wageningen, Netherlands.
    Selective recovery of nickel over iron from a nickel-iron solution using microbial sulfate reduction in a gas-lift bioreactor.2009In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 43, no 3, p. 853-861Article in journal (Refereed)
    Abstract [en]

    Process streams with high concentrations of metals and sulfate are characteristic for the mining and metallurgical industries. This study aims to selectively recover nickel from a nickel-iron-containing solution at pH 5.0 using a single stage bioreactor that simultaneously combines low pH sulfate reduction and metal-sulfide formation. The results show that nickel was selectively precipitated in the bioreactor at pH 5.0 and the precipitates consisted of >or=83% of the nickel content. The nickel-iron precipitates were partly crystalline and had a metal/sulfur ratio of 1, suggesting these precipitates were NiS and FeS. Experiments focusing on nickel recovery at pH 5.0 and 5.5 reached a recovery of >99.9%, resulting in a nickel effluent concentration<0.05 microM. The mixed microbial population included known sulfate reducers and acetogens. This study shows that selective metal precipitation in a single stage sulfate reducing bioreactor operated at low pH has the potential to produce metal-sulfides that can be used by the metallurgical industry as a resource for metal production.

  • 12.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Abbtesaim, Jawad
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wu, Xiaofen
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Copenhagen, Denmark.
    Christel, Stephan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ni, Gaofeng
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lopez-Fernandez, Margarita
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sundkvist, Jan-Eric
    Boliden Mineral AB.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor2017In: Biodegradation, ISSN 0923-9820, E-ISSN 1572-9729, Vol. 28, no 4, p. 287-301Article in journal (Refereed)
    Abstract [en]

    Wastewaters generated during mining and processing of metal sulfide ores are often acidic (pH < 3) and can contain significant concentrations of nitrate, nitrite, and ammonium from nitrogen based explosives. In addition, wastewaters from sulfide ore treatment plants and tailings ponds typically contain large amounts of inorganic sulfur compounds, such as thiosulfate and tetrathionate. Release of these wastewaters can lead to environmental acidification as well as an increase in nutrients (eutrophication) and compounds that are potentially toxic to humans and animals. Waters from cyanidation plants for gold extraction will often conjointly include toxic, sulfur containing thiocyanate. More stringent regulatory limits on the release of mining wastes containing compounds such as inorganic sulfur compounds, nitrate, and thiocyanate, along the need to increase production from sulfide mineral mining calls for low cost techniques to remove these pollutants under ambient temperatures (approximately 8 °C). In this study, we used both aerobic and anaerobic continuous cultures to successfully couple inorganic sulfur compound (i.e. thiosulfate and thiocyanate) oxidation for the removal of nitrogenous compounds under neutral to acidic pH at the low temperatures typical for boreal climates. Furthermore, the development of the respective microbial communities was identified over time by DNA sequencing, and found to contain a consortium including populations aligning within Flavobacterium, Thiobacillus, and Comamonadaceae lineages. This is the first study to remediate mining waste waters by coupling autotrophic thiocyanate oxidation to nitrate reduction at low temperatures and acidic pH by means of an identified microbial community.

  • 13.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Brüsin, Martin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hylander, Samuel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Oxygenation of anoxic sediments triggers hatching of zooplankton eggs2015In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, no 1817, article id 20152025Article in journal (Refereed)
    Abstract [en]

    Many coastal marine systems have extensive areas with anoxic sediments and it is not well known how these conditions affect the benthic-pelagic coupling. Zooplankton lay their eggs in the pelagic zone, and some sink and lie dormant in the sediment, before hatched zooplankton return to the water column. In this study, we investigated how oxygenation of long-term anoxic sediments affects the hatching frequency of dormant zooplankton eggs. Anoxic sediments from the brackish Baltic Sea were sampled and incubated for 26 days with constant aeration whereby, the sediment surface and the overlying water were turned oxic. Newly hatched rotifers and copepod nauplii (juveniles) were observed after 5 and 8 days, respectively. Approximately 1.5 × 105 nauplii per m-2 emerged from sediment turned oxic compared to 0.02 × 105 m-2 from controls maintained anoxic. This study demonstrated that re-oxygenation of anoxic sediments activated a large pool of buried zooplankton eggs, strengthening the benthic-pelagic coupling of the system. Modelling of the studied anoxic zone suggested that a substantial part of the pelagic copepod population can derive from hatching of dormant eggs. We suggest that this process should be included in future studies to understand population dynamics and carbon flows in marine pelagic systems.

  • 14.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Li, Lingni
    Fridlund, Jimmy
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Svensson, Fredrik
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Eutrophication induced early stage hypoxic ‘dead zone’ sediment releases nitrate and stimulates growth of archaeaManuscript (preprint) (Other academic)
    Abstract [en]

    In the Baltic Sea, two annual algal blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water column, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen, referred to as ‘dead zones’). These zones prevent the establishment of benthic communities and result in fish mortality. The aim of the study was to determine how the sediment chemistry and microbial community composition changed due to phytoplankton biomass degradation by adding cyanobacterial or diatom biomass to sediment cores from an all-year round oxic coastal Baltic Sea bay. After biomass addition, some typical anaerobic microbial processes were observed such as a decrease in NO2-+NO3- in the sediment surface (0-1 cm) and iron in the underlying layer (1-2 cm). In addition, an increase in NO2-+NO3- was observed in the water phase in all incubations (including controls without addition of phytoplankton biomass). The combination of NO2-+NO3- diffusion from the sediment plus nitrification of the available NH4+ could not account for this increase. Potential nitrogen sources that could at least partially explain this discrepancy included microbial nitrogen fixation and cycling of nitrogen compounds from deeper layers of the sediment. Based on 16S rRNA gene sequences, the addition of diatom biomass caused minor changes in the relative abundance of microbial community members while cyanobacterial biomass caused a large increase in ferrous iron-oxidizing archaea. Considering that OTUs sharing lineages with acidophilic microorganisms were present, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling in oxic sediments and early microbial community changes in the sediment surface due to sinking phytoplankton before major hypoxia events occur. The release of nitrate into the water could potentially enhance algal blooms and facilitate the development of ‘dead zones’.

  • 15.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Li, Lingni
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Fridlund, Jimmy
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Svensson, Fredrik
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure2019In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, no 2, p. 288-303Article in journal (Refereed)
    Abstract [en]

    Two annual Baltic Sea phytoplankton blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen). These zones prevent the establishment of benthic communities and may result in fish mortality. The aim of the study was to determine how the spring and autumn sediment chemistry and microbial community composition changed due to degradation of diatom or cyanobacterial biomass, respectively. Results from incubation of sediment cores showed some typical anaerobic microbial processes after biomass addition such as a decrease in NO2 + NO3 in the sediment surface (0–1 cm) and iron in the underlying layer (1–2 cm). In addition, an increase in NO2 + NO3 was observed in the overlying benthic water in all amended and control incubations. The combination of NO2 + NO3 diffusion plus nitrification could not account for this increase. Based on 16S rRNA gene sequences, the addition of cyanobacterial biomass during autumn caused a large increase in ferrous iron-oxidizing archaea while diatom biomass amendment during spring caused minor changes in the microbial community. Considering that OTUs sharing lineages with acidophilic microorganisms had a high relative abundance during autumn, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling and early microbial community changes in the sediment due to sinking phytoplankton before potential hypoxia occurs.

  • 16.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sachpazidou, Varvara
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hylander, Samuel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1864, article id 20171617Article in journal (Refereed)
    Abstract [en]

    An important characteristic of marine sediments is the oxygen concentration that affects many central metabolic processes. There has been a widespread increase in hypoxia in coastal systems (referred to as 'dead zones') mainly caused by eutrophication. Hence, it is central to understand the metabolism and ecology of eukaryotic life in sediments during changing oxygen conditions. Therefore, we sampled coastal 'dead zone' Baltic Sea sediment during autumn and spring, and analysed the eukaryotic metatranscriptome from field samples and after incubation in the dark under oxic or anoxic conditions. Bacillariophyta (diatoms) dominated the eukaryotic metatranscriptome in spring and were also abundant during autumn. A large fraction of the diatom RNA reads was associated with the photosystems suggesting a constitutive expression in darkness. Microscope observation showed intact diatom cells and these would, if hatched, represent a significant part of the pelagic phytoplankton biomass. Oxygenation did not significantly change the relative proportion of diatoms nor resulted in any major shifts in metabolic 'signatures'. By contrast, diatoms rapidly responded when exposed to light suggesting that light is limiting diatom development in hypoxic sediments. Hence, it is suggested that diatoms in hypoxic sediments are on 'standby' to exploit the environment if they reach suitable habitats.

  • 17.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sachpazidou, Varvara
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism2017In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, article id 2453Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea has undergone severe eutrophication during the last century, resulting in increased algal blooms and the development of hypoxic bottom waters. In this study, we sampled oxygen deficient sediment cores from a Baltic Sea coastal bay and exposed the bottom water including the sediment surface to oxygen shifts via artificial addition of air during laboratory incubation. Surface sediment (top 1 cm) from the replicate cores were sliced in the field as well as throughout the laboratory incubations and chemical parameters were analyzed along with high throughput sequencing of community DNA and RNA. After oxygenation, dissolved iron decreased in the water overlying the sediment while inorganic sulfur compounds (thiosulfate and tetrathionate) increased when the water was kept anoxic. Oxygenation of the sediment also maintained RNA transcripts attributed to sulfide and sulfur oxidation as well as nitrogen fixation in the sediment surface. Based on 16S rRNA gene and metatranscriptomic analyses it was found that oxygenation of the sediment surface caused a bloom of the Epsilonproteobacteria genus Arcobacter. In addition, the formation of a thick white film was observed that was likely filamentous zero-valent sulfur produced by the Arcobacter spp. Based on these results, sulfur cycling and nitrogen fixation that were evident in the field samples were ongoing during re-oxygenation of the sediment. These processes potentially added organic nitrogen to the system and facilitated the re-establishment of micro- and macroorganism communities in the benthic zone.

  • 18.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sjöstedt, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund university;Tech Univ Denmark, Denmark.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism2017In: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 5, article id 96Article in journal (Refereed)
    Abstract [en]

    Background

    A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as ‘dead zones’. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface.

    Results

    Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation.

    Conclusions

    These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.

  • 19.
    Buetti-Dinh, Antoine
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Dethlefsen, Olga
    Stockholm University.
    Friedman, Ran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes2016In: Microbiology, ISSN 1350-0872, E-ISSN 1465-2080, Vol. 162, no 8, p. 1422-1434Article in journal (Refereed)
    Abstract [en]

    Extremely acidophilic microorganisms (optimum growth pH of ≤3) maintain a near neutral cytoplasmic pH via several homeostatic mechanisms, including an inside positive membrane potential created by potassium ions. Transcriptomic responses to pH stress in the thermoacidophilic archaeon, Sulfolobus acidocaldarius were investigated by growing cells without added sodium and/or potassium ions at both optimal and sub-optimal pH. Culturing the cells in the absence of added sodium or potassium ions resulted in a reduced growth rate compared to full-salt conditions as well as 43 and 75 significantly different RNA transcript ratios, respectively. Differentially expressed RNA transcripts during growth in the absence of added sodium ions included genes coding for permeases, a sodium/proline transporter and electron transport proteins. In contrast, culturing without added potassium ions resulted in higher RNA transcripts for similar genes as a lack of sodium ions plus genes related to spermidine that has a general role in response to stress and a decarboxylase that potentially consumes protons. The greatest RNA transcript response occurred when S. acidocaldarius cells were grown in the absence of potassium and/or sodium at a sub-optimal pH. These adaptations included those listed above plus osmoregulated glucans and mechanosensitive channels that have previously been shown to respond to osmotic stress. In addition, data analyses revealed two co-expressed IclR family transcriptional regulator genes with a previously unknown role in the S. acidocaldarius pH stress response. Our study provides additional evidence towards the importance of potassium in acidophile growth at acidic pH.

  • 20.
    Buetti-Dinh, Antoine
    et al.
    Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Galli, Vanni
    University of Applied Sciences of Southern Switzerland, Switzerland.
    Bellenberg, Sören
    Universität Duisburg-Essen, Germany.
    Ilie, Olga
    Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Herold, Malte
    University of Luxembourg, Luxembourg.
    Christel, Stephan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Boretska, Mariia
    Universität Duisburg-Essen, Germany.
    Pivkin, Igor V.
    Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Wilmes, Paul
    University of Luxembourg, Luxembourg.
    Sand, Wolfgang
    Universität Duisburg-Essen, Germany;Donghua University, People's Republic of China;Mining Academy and Technical University Freiberg, Germany.
    Vera, Mario
    Pontificia Universidad Católica de Chile, Chile.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition2019In: Biotechnology Reports, ISSN 0156-1383, E-ISSN 2215-017X, Vol. 22, p. 1-5, article id e00321Article in journal (Refereed)
    Abstract [en]

    Background: Deep neural networks have been successfully applied to diverse fields of computer vision. However, they only outperform human capacities in a few cases. Methods: The ability of deep neural networks versus human experts to classify microscopy images was tested on biofilm colonization patterns formed on sulfide minerals composed of up to three different bioleaching bacterial species attached to chalcopyrite sample particles. Results: A low number of microscopy images per category (<600) was sufficient for highly efficient computational analysis of the biofilm's bacterial composition. The use of deep neural networks reached an accuracy of classification of ∼90% compared to ∼50% for human experts. Conclusions: Deep neural networks outperform human experts’ capacity in characterizing bacterial biofilm composition involved in the degradation of chalcopyrite. This approach provides an alternative to standard, time-consuming biochemical methods. © 2019 The Author

  • 21.
    Bunse, Carina
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Karlsson, Christofer M. G.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Akram, Neelam
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Vila-Costa, Maria
    Centre d’Estudis Avançats de Blanes-CSIC, Spain.
    Palovaara, Joakim
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Svensson, Lovisa
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Holmfeldt, Karin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    González, José M.
    University of La Laguna, Spain.
    Calvo, Eva
    Institut de Ciències del Mar—CSIC, Spain.
    Pelejero, Carles
    Institut de Ciències del Mar—CSIC, Spain.
    Marrasé, Cèlia
    Institut de Ciències del Mar—CSIC, Spain.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Gasol, Josep
    Institut de Ciències del Mar—CSIC, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Response of marine bacterioplankton pH homeostasis gene expression to elevated CO22016In: Nature Climate Change, ISSN 1758-678X, E-ISSN 1758-6798, Vol. 6, no 5, p. 483-487Article in journal (Refereed)
    Abstract [en]

    Human-induced ocean acidification impacts marine life. Marine bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes1; hence, understanding their performance under projected climate change scenarios is crucial for assessing ecosystem functioning. Whereas genetic and physiological responses of phytoplankton to ocean acidification are being disentangled2, 3, 4, corresponding functional responses of bacterioplankton to pH reduction from elevated CO2 are essentially unknown. Here we show, from metatranscriptome analyses of a phytoplankton bloom mesocosm experiment, that marine bacteria responded to lowered pH by enhancing the expression of genes encoding proton pumps, such as respiration complexes, proteorhodopsin and membrane transporters. Moreover, taxonomic transcript analysis showed that distinct bacterial groups expressed different pH homeostasis genes in response to elevated CO2. These responses were substantial for numerous pH homeostasis genes under low-chlorophyll conditions (chlorophyll a <2.5 μg l−1); however, the changes in gene expression under high-chlorophyll conditions (chlorophyll a >20 μg l−1) were low. Given that proton expulsion through pH homeostasis mechanisms is energetically costly, these findings suggest that bacterioplankton adaptation to ocean acidification could have long-term effects on the economy of ocean ecosystems.

  • 22. Christel, S
    et al.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Vera, M
    Sand, W
    Herold, M
    Wilmes, P
    Buetti-Dinh, Antoine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Pivkin, I
    Trötschel, C
    Poetsch, A
    Nygren, J
    Kubista, M
    Systems Biology of Acidophile Biofilms for Efficient Metal Extraction2015In: Biotechnologies in Mining Industry and Environmental Engineering / [ed] M. Zaki Mubarok, Siti Khodijah Chaerun, Wahyudin Prawira Minwal, Fadhli Muhammad and Killang Pratama, 2015, p. 312-315Conference paper (Refereed)
    Abstract [en]

    This European Union ERASysApp funded study will investigate one of the major drawbacks of bioleaching of the copper containing mineral chalcopyrite, namely the long lag phase between construction and inoculation of bioleaching heaps and the release of dissolved metals. In practice, this lag phase can be up to three years and the long time period adds to the operating expenses of bioheaps for chalcopyrite dissolution. One of the major time determining factors in bioleaching heaps is suggested to be the speed of mineral colonization by the acidophilic microorganisms present. By applying confocal microscopy, metatranscriptomics, metaproteomics, bioinformatics, and computer modeling the authors aim to investigate the processes leading up to, and influencing the attachment of three moderately thermophilic sulfur-and/or iron-oxidizing model species:Acidithiobacillus caldusLeptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans. Stirred tank reactors containing chalcopyrite concentrate will be inoculated with these species in various orders and proportions and the effects on the lag phase and rates of metal release will be compared. Meanwhile, confocal microscopy studies of cell attachment to chalcopyrite mineral particles, as well as metatranscriptomics and metaproteomics of the formed biofilms will further increase understanding of the attachment process and help develop a model thereof. By fulfilling our goal to decrease the length of the lag phase of chalcopyrite bioleaching heaps we hope to increase their economic feasibility and therefore, industrial interest in bioleaching as a sustainable technology.

  • 23.
    Christel, Stephan
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Fridlund, Jimmy
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Buetti-Dinh, Antoine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Buck, Moritz
    Uppsala University.
    Watkin, Elizabeth L.
    Curtin University, Australia.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans2016In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 363, no 7, article id fnw057Article in journal (Refereed)
    Abstract [en]

    Acidithiobacillus ferrivorans is an acidophile implicated in low-temperature biomining for the recovery of metals from sulfide minerals. Acidithiobacillus ferrivorans obtains its energy from the oxidation of inorganic sulfur compounds, and genes encoding several alternative pathways have been identified. Next-generation sequencing of At. ferrivorans RNA transcripts identified the genes coding for metabolic and electron transport proteins for energy conservation from tetrathionate as electron donor. RNA transcripts suggested that tetrathionate was hydrolyzed by the tetH1 gene product to form thiosulfate, elemental sulfur and sulfate. Despite two of the genes being truncated, RNA transcripts for the SoxXYZAB complex had higher levels than for thiosulfate quinone oxidoreductase (doxDA genes). However, a lack of heme-binding sites in soxX suggested that DoxDA was responsible for thiosulfate metabolism. Higher RNA transcript counts also suggested that elemental sulfur was metabolized by heterodisulfide reductase (hdr genes) rather than sulfur oxygenase reductase (sor). The sulfite produced as a product of heterodisulfide reductase was suggested to be oxidized by a pathway involving the sat gene product or abiotically react with elemental sulfur to form thiosulfate. Finally, several electron transport complexes were involved in energy conservation. This study has elucidated the previously unknown At. ferrivorans tetrathionate metabolic pathway that is important in biomining.

  • 24.
    Christel, Stephan
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Fridlund, Jimmy
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Watkin, Elizabeth L.
    Curtin Univ, Australia.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 A degrees C suggesting it is a eurypsychrophile2016In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 20, no 6, p. 903-913Article in journal (Refereed)
    Abstract [en]

    Acidithiobacillus ferrivorans is an acidophilic bacterium that represents a substantial proportion of the microbial community in a low temperature mining waste stream. Due to its ability to grow at temperatures below 15 A degrees C, it has previously been classified as 'psychrotolerant'. Low temperature-adapted microorganisms have strategies to grow at cold temperatures such as the production of cold acclimation proteins, DEAD/DEAH box helicases, and compatible solutes plus increasing their cellular membrane fluidity. However, little is known about At. ferrivorans adaptation strategies employed during culture at its temperature extremes. In this study, we report the transcriptomic response of At. ferrivorans SS3 to culture at 8 A degrees C compared to 20 A degrees C. Analysis revealed 373 differentially expressed genes of which, the majority were of unknown function. Only few changes in transcript counts of genes previously described to be cold adaptation genes were detected. Instead, cells cultured at cold (8 A degrees C) altered the expression of a wide range of genes ascribed to functions in transcription, translation, and energy production. It is, therefore, suggested that a temperature of 8 A degrees C imposed little cold stress on At. ferrivorans, underlining its adaptation to growth in the cold as well as suggesting it should be classified as a 'eurypsychrophile'.

  • 25.
    Christel, Stephan
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Herold, Malte
    University of Luxembourg, Luxembourg.
    Bellenberg, Sören
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Universität Duisburg-Essen, Germany.
    Buetti-Dinh, Antoine
    Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics (SIB), Switzerland.
    El Hajjami, Mohamed
    Ruhr-Universität Bochum, Germany.
    Pivkin, Igor
    Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics (SIB), Switzerland.
    Sand, Wolfgang
    Universität Duisburg-Essen, Germany;Donghua University, Peoples Republic of China;Mining Academy, Germany;Technical University Freiberg, Germany.
    Wilmes, Paul
    University of Luxembourg, Luxembourg.
    Poetsch, Ansgar
    Ruhr-Universität Bochum, Germany;Plymouth University, United Kingdom.
    Vera, Mario
    Pontificia Universidad Católica de Chile, Chile.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Weak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching2018In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 3059Article in journal (Refereed)
    Abstract [en]

    Bioleaching is an emerging technology, describing the microbially assisted dissolution of sulfidicores that provides a more environmentally friendly alternative to many traditional metal extractionmethods, such as roasting or smelting. Industrial interest increases steadily and today, circa 15-20%of the world’s copper production can be traced back to this method. However, bioleaching of theworld’s most abundant copper mineral chalcopyrite suffers from low dissolution rates, oftenattributed to passivating layers, which need to be overcome to use this technology to its full potential.To prevent these passivating layers from forming, leaching needs to occur at a lowoxidation/reduction potential (ORP), but chemical redox control in bioleaching heaps is difficult andcostly. As an alternative, selected weak iron-oxidizers could be employed that are incapable ofscavenging exceedingly low concentrations of iron and therefore, raise the ORP just above the onsetof bioleaching, but not high enough to allow for the occurrence of passivation. In this study, wereport that microbial iron oxidation by Sulfobacillus thermosulfidooxidans meets these specifications.Chalcopyrite concentrate bioleaching experiments with S. thermosulfidooxidans as the sole ironoxidizer exhibited significantly lower redox potentials and higher release of copper compared tocommunities containing the strong iron oxidizer Leptospirillum ferriphilum. Transcriptomic responseto single and co-culture of these two iron oxidizers was studied and revealed a greatly decreasednumber of mRNA transcripts ascribed to iron oxidation in S. thermosulfidooxidans when cultured inthe presence of L. ferriphilum. This allowed for the identification of genes potentially responsible forS. thermosulfidooxidans’ weaker iron oxidation to be studied in the future, as well as underlined theneed for mechanisms to control the microbial population in bioleaching heaps

  • 26.
    Christel, Stephan
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Herold, Malte
    University of Luxembourg, Luxembourg.
    Bellenberg, Sören
    Universität Duisburg-Essen, Germany.
    El Hajjami, Mohamed
    Ruhr Universität Bochum, Germany.
    Buetti-Dinh, Antoine
    Università della Svizzera Italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Pivkine, Igor V.
    Università della Svizzera Italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Sand, Wolfgang
    Universität Duisburg-Essen, Germany;Donghua UniversityMining Academy and Technical University Freiberg, Germany, PR China;.
    Wilmes, Paul
    University of Luxembourg, Luxembourg.
    Poetsch, Ansgar
    Ruhr Universität Bochum, Germany;Plymouth University, UK.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilumT2018In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 4, no 3, article id UNSP e02091-17Article in journal (Refereed)
    Abstract [en]

    Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilumT applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilumT DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as substrate and bioleaching cultures containing chalcopyrite (CuFeS2). Leptospirillum ferriphilumT adaptations to growth on chalcopyrite included a possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, expression and translation of genes responsible for chemotaxis and motility were enhanced.

  • 27.
    Christel, Stephan
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Yu, Changxun
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wu, Xiaofen
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Josefsson, Sarah
    Geological Survey of Sweden, Sweden.
    Lillhonga, Tom
    Novia University of Applied Sciences, Finland.
    Högfors-Rönnholm, Eva
    Novia University of Applied Sciences, Finland.
    Sohlenius, Gustav
    Geological Survey of Sweden, Sweden.
    Åström, Mats E.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Comparison of Boreal Acid Sulfate Soil Microbial Communities in Oxidative and Reductive Environments2019In: Research in Microbiology, ISSN 0923-2508, E-ISSN 1769-7123, Vol. 170, no 6-7, p. 288-295Article in journal (Refereed)
    Abstract [en]

    Due to land uplift after the last ice age, previously stable Baltic Sea sulfidic sediments are becoming dry land. When these sediments are drained, the sulfide minerals are exposed to air and can release large amounts of metals and acid into the environment. This can cause severe ecological damage such as fish kills in rivers feeding the northern Baltic Sea. In this study, five sites were investigated for the occurrence of acid sulfate soils and their geochemistry and microbiology was identified. The pH and soil chemistry identified three of the areas as having classical acid sulfate soil characteristics and culture independent identification of 16S rRNA genes identified populations related to acidophilic bacteria capable of catalyzing sulfidic mineral dissolution, including species likely adapted to low temperature. These results were compared to an acid sulfate soil area that had been flooded for ten years and showed that the previously oxidized sulfidic materials had an increased pH compared to the unremediated oxidizied layers. In addition, the microbiology of the flooded soil had changed such that alkalinity producing ferric and sulfate reducing reactions had likely occurred. This suggested that flooding of acid sulfate soils mitigates their environmental impact.

  • 28.
    Dar, Shabir A
    et al.
    Umeå University.
    Bijmans, Martijn F M
    Univ Wageningen & Res Ctr, Wageningen, Netherlands.
    Dinkla, Inez J T
    Bioclear BV, NL-9704 CG Groningen, Netherlands.
    Geurkink, Bert
    Bioclear BV, NL-9704 CG Groningen, Netherlands.
    Lens, Piet N L
    Univ Wageningen & Res Ctr, Wageningen, Netherlands.
    Dopson, Mark
    Umeå University.
    Population dynamics of a single-stage sulfidogenic bioreactor treating synthetic zinc-containing waste streams.2009In: 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.

  • 29.
    Dopson, Mark
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Physiological adaptations and biotechnological applications of acidophiles2012In: Extremophiles: Microbiology and Biotechnology / [ed] Anitori RP, Norfolk UK: Caister Academic Press, 2012, p. 265-294Chapter in book (Refereed)
  • 30.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Physiological and phylogenetic diversity of acidophilic bacteria2016In: Acidophiles: life in extremely acidic environments / [ed] Quatrini R & Johnson DB, Caister Academic Press, 2016, p. 79-92Chapter in book (Refereed)
    Abstract [en]

    Acidophilic bacteria can be found in natural and anthropogenic acidic environments such as acid sulfate soils and biomining operations. These environments range in temperatures from below zero where low temperature adapted, acidophilic bacteria accelerate metal and acid release from sulfide minerals, through mesophilic environments, to hot solfataric fields containing Hydrogenobaculum acidophilum with a temperature optimum of 65°C. Acidophilic bacteria have been isolated from the ActinobacteriaAquificaeFirmicutesNitropsoraProteobacteria, and Verrucomicrobia phyla, and are capable of oxidizing both inorganic and organic electron donors coupled to the reduction of oxygen or ferric iron, though no extremely acidophilic bacteria are known to ferment organic substrates. Acidophilic bacteria also exhibit a range of carbon metabolisms, from obligate autotrophs such as Leptospirillum spp., facultative autotrophs such as Sulfobacillus spp. that can both fix carbon dioxide (CO2) or assimilate organic carbon, to obligate heterotrophs such as Alicyclobacillus tolerans. This chapter summarizes present knowledge of the physiological and phylogenetic diversity of acidophilic bacteria and highlights differences in growth characteristics between the various species.

  • 31.
    Dopson, Mark
    et al.
    Umeå University ; University of East Anglia, Norwich, UK.
    Baker-Austin, Craig
    University of East Anglia, Norwich, UK ; University of Georgia, Aiken, SC, USA.
    Bond, Philip
    University of East Anglia, Norwich, UK ; Advanced Wastewater Management Centre, University of Queensland, Queensland, Australia.
    Towards determining details of anaerobic growth coupled to ferric iron reduction by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.2007In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 11, no 1, p. 159-168Article 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.

  • 32.
    Dopson, Mark
    et al.
    University of East Anglia, Norwich, UK.
    Baker-Austin, Craig
    University of East Anglia, Norwich, UK.
    Bond, Philip L
    University of East Anglia, Norwich, UK.
    Analysis of differential protein expression during growth states of Ferroplasma strains and insights into electron transport for iron oxidation.2005In: Microbiology, ISSN 1350-0872, E-ISSN 1465-2080, Vol. 151, no 12, p. 4127-4137Article 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.

  • 33.
    Dopson, Mark
    et al.
    University of East Anglia, Norwich, United Kingdom.
    Baker-Austin, Craig
    University of East Anglia, Norwich, United Kingdom.
    Hind, Andrew
    University of East Anglia, Norwich, United Kingdom.
    Bowman, John P
    University of Tasmania, Hobart, Tasmania, Australia.
    Bond, Philip L
    University of East Anglia, Norwich, United Kingdom.
    Characterization of Ferroplasma isolates and Ferroplasma acidarmanus sp. nov., extreme acidophiles from acid mine drainage and industrial bioleaching environments.2004In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 70, no 4, p. 2079-2088Article 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.

  • 34.
    Dopson, Mark
    et al.
    University of East Anglia, Norwich, UK.
    Baker-Austin, Craig
    University of East Anglia, Norwich, UK.
    Koppineedi, P Ram
    University of East Anglia, Norwich, UK.
    Bond, Philip L
    University of East Anglia, Norwich, UK.
    Growth in sulfidic mineral environments: metal resistance mechanisms in acidophilic micro-organisms.2003In: Microbiology, ISSN 1350-0872, E-ISSN 1465-2080, Vol. 149, no 8, p. 1959-1970Article in journal (Refereed)
    Abstract [en]

    Acidophilic micro-organisms inhabit some of the most metal-rich environments known, including both natural and man-made ecosystems, and as such are ideal model systems for study of microbial metal resistance. Although metal resistance systems have been studied in neutrophilic micro-organisms, it is only in recent years that attention has been placed on metal resistance in acidophiles. The five metal resistance mechanisms identified in neutrophiles are also present in acidophiles, in some cases utilizing homologous proteins, but in many cases the degree of resistance is greater in acidophiles. This review summarizes the knowledge of acidophile metal resistance and presents preliminary in silico studies on a few known metal resistance systems in the sequenced acidophile genomes.

  • 35.
    Dopson, Mark
    et al.
    University of East Anglia, Norwich, UK.
    Baker-Austin, Craigh
    University of East Anglia, Norwich, UK.
    Bond, Philip. L.
    University of East Anglia, Norwich, UK.
    First use of two-dimensional polyacrylamide gel electrophoresis to determine phylogenetic relationships2004In: Journal of Microbiological Methods, ISSN 0167-7012, E-ISSN 1872-8359, 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.

  • 36.
    Dopson, Mark
    et al.
    Umeå University.
    Halinen, A.-K.
    Tampere Univ Technol, Finland.
    Rahunen, N.
    Tampere Univ Technol, Finland.
    Boström, Dan
    Umeå University.
    Sundkvist, J.-E.
    Boliden Mineral AB, Boliden, Sweden.
    Riekkola-Vanhanen, M.
    Talvivaara Project Ltd, Sotkamo, Finland.
    Kaksonen, A.H.
    Tampere Univ Technol, Finland.
    Puhakka, J. A.
    Tampere Univ Technol, Finland.
    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 dissolutionsuch 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.

  • 37.
    Dopson, Mark
    et al.
    Umeå University.
    Halinen, Anna-Kaisa
    Tampere University of Technology, Tampere, Finland.
    Rahunen, Nelli
    Tampere University of Technology, Tampere, Finland.
    Özkaya, Bestamin
    Tampere University of Technology, Tampere, Finland.
    Sahinkaya, Erkan
    Tampere University of Technology, Tampere, Finland.
    Kaksonen, Anna H
    Tampere University of Technology, Tampere, Finland.
    Lindström, E Börje
    Umeå University.
    Puhakka, Jaakko A
    Tampere University of Technology, Tampere, Finland.
    Mineral and iron oxidation at low temperatures by pure and mixed cultures of acidophilic microorganisms.2007In: Biotechnology and Bioengineering, ISSN 0006-3592, E-ISSN 1097-0290, Vol. 97, no 5, p. 1205-1215Article 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.

  • 38.
    Dopson, Mark
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Holmes, David S
    Universidad Andres Bello, Santiago, Chile.
    Metal resistance in acidophilic microorganisms and its significance for biotechnologies.2014In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 98, no 19, p. 8133-8144Article in journal (Refereed)
    Abstract [en]

    Extremely acidophilic microorganisms have an optimal pH of <3 and are found in all three domains of life. As metals are more soluble at acid pH, acidophiles are often challenged by very high metal concentrations. Acidophiles are metal-tolerant by both intrinsic, passive mechanisms as well as active systems. Passive mechanisms include an internal positive membrane potential that creates a chemiosmotic gradient against which metal cations must move, as well as the formation of metal sulfate complexes reducing the concentration of the free metal ion. Active systems include efflux proteins that pump metals out of the cytoplasm and conversion of the metal to a less toxic form. Acidophiles are exploited in a number of biotechnologies including biomining for sulfide mineral dissolution, biosulfidogenesis to produce sulfide that can selectively precipitate metals from process streams, treatment of acid mine drainage, and bioremediation of acidic metal-contaminated milieux. This review describes how acidophilic microorganisms tolerate extremely high metal concentrations in biotechnological processes and identifies areas of future work that hold promise for improving the efficiency of these applications.

  • 39.
    Dopson, Mark
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Holmes, David S.
    Andrés Bello National University, Chile;Fundación Ciencia & Vida, Chile.
    Lazcano, Marcelo
    Andrés Bello National University, Chile;Fundación Ciencia & Vida, Chile.
    McCredden, Timothy J.
    Curtin University, Australia.
    Bryan, Christopher G.
    Curtin University, Australia.
    Mulroney, Kieran T.
    Curtin University, Australia.
    Steuart, Robert
    Curtin University, Australia.
    Jackaman, Connie
    Curtin University, Australia.
    Watkin, Elizabeth L. J.
    Curtin University, Australia.
    Multiple Osmotic Stress Responses in Acidihalobacter prosperus Result in Tolerance to Chloride Ions2017In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, article id 2132Article in journal (Refereed)
    Abstract [en]

    Extremely acidophilic microorganisms (pH optima for growth of <= 3) are utilized for the extraction of metals from sulfide minerals in the industrial biotechnology of biomining. A long term goal for biomining has been development of microbial consortia able to withstand increased chloride concentrations for use in regions where freshwater is scarce. However, when challenged by elevated salt, acidophiles experience both osmotic stress and an acidification of the cytoplasm due to a collapse of the inside positive membrane potential, leading to an influx of protons. In this study, we tested the ability of the halotolerant acidophile Acidihalobacter prosperus to grow and catalyze sulfide mineral dissolution in elevated concentrations of salt and identified chloride tolerance mechanisms in Ac. prosperus as well as the chloride susceptible species, Acidithiobacillus ferrooxidans. Ac. prosperus had optimum iron oxidation at 20 g L-1 NaCl while At. ferrooxidans iron oxidation was inhibited in the presence of 6 g L-1 NaCl. The tolerance to chloride in Ac. prosperus was consistent with electron microscopy, determination of cell viability, and bioleaching capability. The Ac. prosperus proteomic response to elevated chloride concentrations included the production of osmotic stress regulators that potentially induced production of the compatible solute, ectoine uptake protein, and increased iron oxidation resulting in heightened electron flow to drive proton export by the F0F1 ATPase. In contrast, At. ferrooxidans responded to low levels of Cl- with a generalized stress response, decreased iron oxidation, and an increase in central carbon metabolism. One potential adaptation to high chloride in the Ac. prosperus Rus protein involved in ferrous iron oxidation was an increase in the negativity of the surface potential of Rus Form I (and Form II) that could help explain how it can be active under elevated chloride concentrations. These data have been used to create a model of chloride tolerance in the salt tolerant and susceptible species Ac. prosperus and At. ferrooxidans, respectively.

  • 40.
    Dopson, Mark
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Johnson, D. Barrie
    Biodiversity, metabolism and applications of acidophilic sulfur-metabolizing microorganisms2012In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 14, no 10, p. 2620-2631Article, review/survey (Refereed)
    Abstract [en]

    Extremely acidic, sulfur-rich environments can be natural, such as solfatara fields in geothermal and volcanic areas, or anthropogenic, such as acid mine drainage waters. Many species of acidophilic bacteria and archaea are known to be involved in redox transformations of sulfur, using elemental sulfur and inorganic sulfur compounds as electron donors or acceptors in reactions involving between one and eight electrons. This minireview describes the nature and origins of acidic, sulfur-rich environments, the biodiversity of sulfur-metabolizing acidophiles, and how sulfur is metabolized and assimilated by acidophiles under aerobic and anaerobic conditions. Finally, existing and developing technologies that harness the abilities of sulfur-oxidizing and sulfate-reducing acidophiles to extract and capture metals, and to remediate sulfur-polluted waste waters are outlined.

  • 41.
    Dopson, Mark
    et al.
    Umeå University.
    Lindstrom, Börje
    Umeå University.
    Potential role of thiobacillus caldus in arsenopyrite bioleaching1999In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 65, no 1, p. 36-40Article in journal (Refereed)
    Abstract [en]

    We investigated the potential role of the three strains of Thiobacillus caldus (KU, BC13, and C-SH12) in arsenopyrite leaching in combination with a moderately thermophilic iron oxidizer, Sulfobacillus thermosulfidooxidans. Pure cultures of T. caldus and S. thermosulfidooxidans were used as well as defined mixed cultures. By measuring released iron, tetrathionate, and sulfur concentrations, we found that the presence of T. caldus KU and BC13 in the defined mixed culture lowered the concentration of sulfur, and levels of tetrathionate were comparable to or lower than those in the presence of S. thermosulfidooxidans. This suggests that T. caldus grows on the sulfur compounds that build up during leaching, increasing the arsenopyrite-leaching efficiency. This result was similar to leaching arsenopyrite with a pure culture of S. thermosulfidooxidans in the presence of yeast extract. Therefore, three possible roles of T. caldus in the leaching environment can be hypothesized: to remove the buildup of solid sulfur that can cause an inhibitory layer on the surface of the mineral, to aid heterotrophic and mixotrophic growth by the release of organic chemicals, and to solubilize solid sulfur by the production of surface-active agents. The results showed that T. caldus KU was the most efficient at leaching arsenopyrite under the conditions tested, followed by BC13, and finally C-SH12.

  • 42.
    Dopson, Mark
    et al.
    Umeå University.
    Lindström, E B
    Umeå University.
    Analysis of community composition during moderately thermophilic bioleaching of pyrite, arsenical pyrite, and chalcopyrite.2004In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 48, no 1, p. 19-28Article in journal (Refereed)
    Abstract [en]

    An analysis of the community composition of three previously undefined mixed cultures of moderately thermophilic bioleaching bacteria grown at 45 degrees C on pyrite, arsenical pyrite, and chalcopyrite has been carried out. The bacterial species present were identified by comparative sequence analysis of the 16S rRNA gene isolated from the bioleaching vessels and analyzed by denaturing gradient gel electrophoresis, cloning, and sequencing. The mixed cultures leached all three minerals, as shown by the increase in iron released from the mineral concentrates. The species identified from the mixed cultures during bioleaching of pyrite, arsenical pyrite, and chalcopyrite were clones closely related to Acidithiobacillus caldus C-SH12, Sulfobacillus thermosulfidooxidans AT-1, " Sulfobacillus montserratensis" L15, and an uncultured thermal soil bacterium YNP. It was also found that the same mixed culture maintained for over a year on chalcopyrite mineral selected approximately the same consortia of bacteria as the original mixed culture grown on chalcopyrite.

  • 43.
    Dopson, Mark
    et al.
    Umeå University.
    Lindström, E B
    Umeå University.
    Hallberg, K B
    Umeå University.
    Chromosomally encoded arsenical resistance of the moderately thermophilic acidophile Acidithiobacillus caldus.2001In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 5, no 4, p. 247-255Article in journal (Refereed)
    Abstract [en]

    Arsenical resistance is important to bioleaching microorganisms because these organisms release arsenic from minerals such as arsenopyrite during bioleaching. The acidophile Acidithiobacillus caldus KU was found to be resistant to the arsenical ions arsenate, arsenite, and antimony via an inducible, chromosomally encoded resistance mechanism. Because no apparent alteration of the toxic ions was observed, Acidithiobacillus (At.) caldus was tested to determine if it was resistant as a result of decreased accumulation of toxic ions. Reduced accumulation of arsenate and arsenite by induced At. caldus cells supported this hypothesis. It was also found that, with the addition of an energy source, induced At. caldus could transport arsenate and arsenite out of the cell against a concentration gradient. The lack of efflux in the absence of an added energy source and in the presence of inhibitors suggested that efflux was energy dependent. Induced At. caldus also expressed arsenate reductase activity, indicating that At. caldus has an arsenical resistance mechanism that is analogous to previously described systems from other Bacteria. Southern hybridization analysis showed that At. caldus and other gram-negative acidophiles carry an Escherichia coli arsB homologue on the chromosome.

  • 44.
    Dopson, Mark
    et al.
    Umeå University.
    Lindström, E Börje
    Umeå University.
    Hallberg, Kevin B
    University of Wales, Bangor, Gwynedd, UK.
    ATP generation during reduced inorganic sulfur compound oxidation by Acidithiobacillus caldus is exclusively due to electron transport phosphorylation.2002In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 6, no 2, p. 123-129Article in journal (Refereed)
    Abstract [en]

    The synthesis of adenosine 5-triphosphate (ATP) (increase in phosphorylation potential) during the oxidation of reduced inorganic sulfur compounds was studied in the moderately thermophilic acidophileAcidithiobacillus caldus (strain KU) (formerly Thiohacillus caldus). The phosphorylation potential increased during the oxidation of all reduced inorganic sulfur compounds tested compared with resting cells. The generation of ATP in whole cells was inhibited by the F0F1 ATPase inhibitor oligomycin, electron transport chain inhibitors, valinomycin and potassium ions. There was no increase in the phosphorylation potential, nor synthesis of ATP. in the absence of electron transport. An apparent lack of substrate-level phosphorylation was indicated by the lack of adenosine 5-phosphosulfate reductase in tetrathionate-grown At. caldus. Studies were also performed on the synthesis of ATP by membrane vesicles of At. caldus when presented with an artificial proton gradient. Complete inhibition of ATP synthesis in these vesicles occurred when they were loaded with N,N-dicyclohexylcarbodiimide (DCCD), but not when they were loaded with oligomycin, vanadate or electron transport chain inhibitors. The data presented here suggest that during the oxidation of reduced inorganic sulfur compounds by At. caldus, all ATP is synthesized by oxidative phosphorylation via a membrane-bound F0F1 ATPase driven by a proton gradient.

  • 45.
    Dopson, Mark
    et al.
    Umeå University.
    Lövgren, Lars
    Umeå University.
    Boström, Dan
    Umeå University.
    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.

  • 46.
    Dopson, Mark
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ni, Gaofeng
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sleutels, Tom H. J. A.
    European Ctr Excellence Sustainable Water Technol, Netherlands.
    Possibilities for extremophilic microorganisms in microbial electrochemical systems2016In: FEMS Microbiology Reviews, ISSN 0168-6445, E-ISSN 1574-6976, Vol. 40, no 2, p. 164-181Article, review/survey (Refereed)
    Abstract [en]

    Microbial electrochemical systems exploit the metabolism of microorganisms to generate electrical energy or a useful product. In the past couple of decades, the application of microbial electrochemical systems has increased from the use of wastewaters to produce electricity to a versatile technology that can use numerous sources for the extraction of electrons on the one hand, while on the other hand these electrons can be used to serve an ever increasing number of functions. Extremophilic microorganisms grow in environments that are hostile to most forms of life and their utilization in microbial electrochemical systems has opened new possibilities to oxidize substrates in the anode and produce novel products in the cathode. For example, extremophiles can be used to oxidize sulfur compounds in acidic pH to remediate wastewaters, generate electrical energy from marine sediment microbial fuel cells at low temperatures, desalinate wastewaters and act as biosensors of low amounts of organic carbon. In this review, we will discuss the recent advances that have been made in using microbial catalysts under extreme conditions and show possible new routes that extremophilic microorganisms open for microbial electrochemical systems.This review highlights the use of microbial electrochemical systems to catalyze environmental processes coupled to the production of energy or valuable resources and how utilizing extremophilic microorganisms opens up new possibilities such as bioremediation of environmentally hazardous wastes.This review highlights the use of microbial electrochemical systems to catalyze environmental processes coupled to the production of energy or valuable resources and how utilizing extremophilic microorganisms opens up new possibilities such as bioremediation of environmentally hazardous wastes.

  • 47.
    Dopson, Mark
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ossandon, Francisco J.
    Universidad Andrés Bello, Chile.
    Lovgren, Lars
    Umeå University.
    Holmes, David S.
    Universidad Andrés Bello, Chile.
    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, article id 157Article 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.

  • 48.
    Dopson, Mark
    et al.
    Umeå University.
    Sundkvist, Jan-Eric
    Boliden Mineral AB, SE-936 81 Boliden, Sweden.
    Lindström, E. Börje
    Umeå University.
    Toxicity of metal extraction and flotation chemicals to Sulfolobus metallicus and chalcopyrite bioleaching2006In: Hydrometallurgy, ISSN 0304-386X, E-ISSN 1879-1158, Vol. 81, no 3-4, p. 205-213Article in journal (Refereed)
    Abstract [en]

    The effect of chemicals used in preparation of mineral concentrates and subsequent extraction of metals to the thermophilic, acidophilic microorganism Sulfolobus metallicus has been tested. The chemicals tested included collectors and frothers employed during flotation of the oreto produce a mineral concentrate, solvent extraction reagents used to remove metals after leaching, and thiocyanate produced as a decomposition product during cyanidation for gold recovery. The effect of these chemicals to S. metallicus depends on the conditions and time frame that the experiments were carried out due to their mode of toxicity and stability in acid pH. The metal extraction chemical that had the least effect on bioleaching was potassium amyl xanthate that increased the leaching rate, possibly due to solubilization of sulfur that can form passivation layers on the surface of minerals. The frother Flotanol C-7 decreased the chalcopyrite leaching rate, despite having no effect on Fe2+ oxidation by S. metallicus resting cells. This is probably due to inhibition of oxygen transfer during bioleaching that had little effect on Fe2+ oxidation over 20 min. Solvent extraction chemicals inhibited both Fe2+ oxidation and bioleaching suggesting their mode of inhibition is due toFe2+ oxidation. The results suggest that relevant concentrations of metal extraction and flotation chemicals can be toxic to chalcopyritebioleaching by S. metallicus.

  • 49.
    Drake, Henrik
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Whitehouse, Martin J.
    Swedish Museum of Natural History.
    Heim, Christine
    Georg August Univ, Germany.
    Reiners, Peter W.
    Univ Arizona, USA.
    Tillberg, Mikael
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hogmalm, K. Johan
    University of Gothenburg.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Broman, Curt
    Stockholm University.
    Åström, Mats E.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Unprecedented 34S-enrichment of pyrite formed following microbial sulfate reduction in fractured crystalline rocks2018In: Geobiology, ISSN 1472-4677, E-ISSN 1472-4669, Vol. 16, no 5, p. 556-574Article in journal (Refereed)
    Abstract [en]

    In the deep biosphere, microbial sulfate reduction (MSR) is exploited for energy. Here, we show that, in fractured continental crystalline bedrock in three areas in Sweden, this process produced sulfide that reacted with iron to form pyrite extremely enriched in S-34 relative to S-32. As documented by secondary ion mass spectrometry (SIMS) microanalyses, the S-34(pyrite) values are up to +132 parts per thousand V-CDT and with a total range of 186 parts per thousand. The lightest S-34(pyrite) values (-54 parts per thousand) suggest very large fractionation during MSR from an initial sulfate with S-34 values (S-34(sulfate,0)) of +14 to +28 parts per thousand. Fractionation of this magnitude requires a slow MSR rate, a feature we attribute to nutrient and electron donor shortage as well as initial sulfate abundance. The superheavy S-34(pyrite) values were produced by Rayleigh fractionation effects in a diminishing sulfate pool. Large volumes of pyrite with superheavy values (+120 +/- 15 parts per thousand) within single fracture intercepts in the boreholes, associated heavy average values up to +75 parts per thousand and heavy minimum S-34(pyrite) values, suggest isolation of significant amounts of isotopically light sulfide in other parts of the fracture system. Large fracture-specific S-34(pyrite) variability and overall average S-34(pyrite) values (+11 to +16 parts per thousand) lower than the anticipated S-34(sulfate,0) support this hypothesis. The superheavy pyrite found locally in the borehole intercepts thus represents a late stage in a much larger fracture system undergoing Rayleigh fractionation. Microscale Rb-Sr dating and U/Th-He dating of cogenetic minerals reveal that most pyrite formed in the early Paleozoic era, but crystal overgrowths may be significantly younger. The C-13 values in cogenetic calcite suggest that the superheavy S-34(pyrite) values are related to organotrophic MSR, in contrast to findings from marine sediments where superheavy pyrite has been proposed to be linked to anaerobic oxidation of methane. The findings provide new insights into MSR-related S-isotope systematics, particularly regarding formation of large fractions of S-34-rich pyrite.

  • 50.
    Esparza, Mario
    et al.
    Univ Antofagasta, Chile.
    Jedlicki, Eugenia
    Fdn Ciencia & Vida, Chile.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Holmes, David S.
    Fdn Ciencia & Vida, Chile ; Univ Andres Bello, Chile.
    Expression and activity of the Calvin-Benson-Bassham cycle transcriptional regulator CbbR from Acidithiobacillus ferrooxidans in Ralstonia eutropha2015In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 362, no 15, article id UNSP fnv108Article in journal (Refereed)
    Abstract [en]

    Autotrophic fixation of carbon dioxide into cellular carbon occurs via several pathways but quantitatively, the Calvin-Benson-Bassham cycle is the most important. CbbR regulates the expression of the cbb genes involved in CO2 fixation via the Calvin-Benson-Bassham cycle in a number of autotrophic bacteria. A gene potentially encoding CbbR (cbbR(AF)) has been predicted in the genome of the chemolithoautotrophic, extreme acidophile Acidithiobacillus ferrooxidans. However, this microorganism is recalcitrant to genetic manipulation impeding the experimental validation of bioinformatic predictions. Two novel functional assays were devised to advance our understanding of cbbR(AF) function using the mutated facultative autotroph Ralstonia eutropha H14 Delta cbbR as a surrogate host to test gene function: (i) cbbR(AF) was expressed in R. eutropha and was able to complement Delta cbbR; and (ii) CbbR(AF) was able to regulate the in vivo activity of four A. ferrooxidans cbb operon promoters in R. eutropha. These results open up the use of R. eutropha as a surrogate host to explore cbbR(AF) activity.

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