Systems Biology of Microorganisms

The "Systems Biology of Extreme Microorganisms" Research Group is part of 'Biology and Environmental Sciences' at Linnaeus University, Kalmar. The group was established in 2010 in the first year that Linnaeus was founded. We use a variety of systems biology techniques to investigate extreme microorganisms and the milieu in which they grow as well as life in the deep biosphere. The data is applied to industrial projects to clean the environment, remove polluting chemicals from industrial process waters, and to investigate how microorganisms affect nutrient and elemental cycles.

You are welcome to browse these pages for details on our past and present studies. Should you have any questions or comments, or if you're interested in joining us as a student or researcher, please contact us using the details given below.

Bioelectrochemical metal recovery for metal production, recycling, and remediation

BioelectroMET is a collaborative EU project that will provide a sustainable alternative for recovery, recycling and remediation of metals from the mining industry. The technology developed in the field of microbial fuel cells will be used to directly convert wastes from the mining industry into electricity for the recovery of metals.

The main aims of this project were:

1. To study the microbial ecology of sulfide mineral mines and acid mine drainage to select suitable candidates for use in a microbial fuel cell.
2. Test the activity of the selected microbes to attach on to the electrodes and their ability to survive in and utilize wastewater to generate electrons and energy.
3. With the combined effort of the consortium, to build a microbial fuel cell which can efficiently and selectively produce, recover, and remediate metals from streams of high and low metal concentrations.
4. Scale up the bioelectrochemical device and demonstrate on-site metal recovery at mining sites or metallurgical plants.

Systems biology of acidophile biofilms for efficient metal extraction

In collaboration with many research groups from all over Europe, this EU funded project will investigate biofilm formation on the surface of the world's most abundant copper mineral, chalcopyrite. By applying con focal microscopy, metatranscriptomics, metaproteomics, bioinformatics, and computer modelling we will model how acidophilic microorganisms interact with the copper mineral and each other. This knowledge will be applied to bioheap inoculation to shorten the lag phase between building industrial bioheaps and the release of copper. In turn, this will increase the economic feasibility and industrial interest in bioleaching as a sustainable technology.

The main aims of this project were:

1. Test the effects of biofilm formation on bacterial metabolism and bioleaching efficiency.
2. Model microbial colonization patterns and interactions within biofilms.
3. Discern the optimal inoculation strategy for efficient biofilm formation.
4. Optimize industrial copper dissolution from chalcopyrite.

Removal of chalcopyrite passivation layers (with Luleå University of Technology)

The copper mineral with the most reserves in the world is chalcopyrite. However, chalcopyrite biomining is hindered by the formation of a barrier layer on the surface, called 'passivation'. The nature of this layer and how it may be removed is being investigated to increase the efficiency of copper solubilization.

The main aims of the project were:

1. Simulate temperature profiles in bioleaching experiments under controlled redox potential in an electrochemical cell and in a redox controlled column reactor.
2. Characterize chalcopyrite surfaces from the different leaching environments by means of X-ray Photoelectron Spectroscopy (XPS) to determine the nature of the passivating layer.Analyze gene and/or protein expression for inorganic sulfur compound and ferrous iron oxidation by acidophilic microorganisms.
3. Test a conceptual flowsheet to remove passivating layers under conditions mimicking stirred tank and heap bioleaching.

Understand how acidophiles are able to grow at low temperature

An acid mine drainage stream biofilm situated 250 m below ground in the permanently cold Kristineberg mine, northern Sweden was investigated to understand how the microbial community is equipped for growth at low temperature and acidic pH. Metagenomic sequencing of the biofilm and planktonic fractions will identify the dominating microorganisms and their metabolic capacities.

The main aims of the project were:

1. Identify the total microbial community including uncultivable species and archaea in Kristineberg mine.
2. Link the potential metabolic pathways to the environmental conditions.Identify acidophile strategies for growth at low temperature.
3. Exploit their ability to grow at low temperature for bioremediation of mining wastewaters.

Biological membranes in extreme conditions: tetraether lipid membranes and their interactions with potassium

Acidophiles are microorganisms that have evolved to live under highly acidic conditions. They have an internal positive membrane potential, which appears to contribute to their metal-resistance and ability to live in acidic conditions. How this potential is generated and maintained is unclear. The interest in the acidophile membrane is not only theoretical – as due to their stability over wide-range of temperatures and acidities the membranes may be useful for biomedical applications (such as drug-carriers). This project is funded by a grant from the Crafoord Foundation and carried out in collaboration with Ran Friedman at Lnu.

The main aims of the project were:

1. Use a computer-aided approach to model the interaction of acidophile membranes with potassium.
2. Create hypotheses as to how potassium generates an internal membrane potential.
3. Test growth at with low and high potassium concentrations in the laboratory.

2019

2018

2017

Christel S, M Herold, S Bellenberg, M El Hajjami, A Buetti-Dinh, IV Pivkin, W Sand, P Wilmes, A Poetsch, M Dopson (2018) Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilum T. Appl Environ Microbiol 3: UNSP e02091-17.

Broman E, V Sachpazidou, J Pinhassi & M Dopson (2017) Oxygenation of hypoxic coastal Baltic Sea sediments impacts on chemistry, microbial community composition, and metabolism. Front Microbiol 8: 2453. doi: 10.3389/fmicb.2017.02453.

Broman E, V Sachpazidou, M Dopson & S Hylander (2017) Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments. Proc Royal Soc B 284: doi: 10.1098/rspb.2017.1617.

Broman, E., Sjöstedt, J., Pinhassi, J., Dopson, M. (2017). Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism. Microbiome. 5: 96.

Broman E, A Jawad, X Wu, S Christel, G Ni, M Lopez-Fernandez, J-E Sundkvist & M Dopson (2017) Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor. Biodegradation 28: 1-15

Wu X, K Pedersen, J Edlund, L Eriksson, M Åström, AF Andersson, S Bertilsson & M Dopson (2017) Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters. Microbiome 5: 37. doi: 10.1186/s40168-017-0253-y.

Abromaitis V, V Racys, P van der Marel, G Ni, M Dopson, AL Wolthuizen, RJW Meulepas (2017) Biofilm development in biological activated carbons systems and its role in activated carbon regeneration: the effect of shear stress and carbon surface roughness. Chem Engin J 317: 503-511.

Dopson M, DS Holmes, M Lazcano, TJ McCredden, C Bryan, KT Mulroney, R Steuart,, C Jackaman, ELJ Watkin (2017) Multiple osmotic stress responses in Acidihalobacter prosperus result in tolerance to chloride ions. Front Microbiol 7:2132. doi: 10.3389/fmicb.2016.02132.

Khoshkhoo M, M Dopson, F Engström & Å Sandström (2017) New insights into the influence of redox potential on chalcopyrite leaching behaviour. Min Engin 100: 9-16.

2016

Roman P, JBM Klok, JAB Sousa, E Broman, M Dopson, E Van Zessen, MFM Bijmans, DY Sorokin, AJH Janssen (2016) Selection and application of sulfide oxidizing microorganisms able to withstand thiols in gas biodesulfurization systems. Environ Sci Technol 50: 12808–12815.

Christel S, J Fridlund, EL Watkin, & M Dopson (2016) Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold shock during growth at 8 °C. Extremophiles 20: 903–913.

De Castro LFP, M Dopson & R Friedman (2016) Biological membranes in extreme conditions: anionic tetraether lipid membranes and their interactions with sodium and potassium. J Physi Chem Part B

Buetti-Dinh A, R Friedman & M Dopson (2016) Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes. Microbiology In-press: doi: 10.1099/mic.0.000314.

De Castro LFP, M Dopson & R Friedman (2016) Biological membranes in extreme conditions: simulations of anionic archaeal tetraether lipid membranes. Plos One 11: e0155287. doi:10.1371/journal.pone.0155287.

Ni G, S Christel, P Roman, ZL Wong, MFM Bijmans & M Dopson (2016) Electricity generation from inorganic sulfur compound containing mining wastewater by acidophilic microorganisms. Res Microbiol. doi:10.1016/j.resmic.2016.04.010.

Christel S, J Fridlund, A Buetti-Dinh, EL Watkin & M Dopson (2016) RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans. FEMS Microbiol Letts 363. doi: 10.1093/femsle/fnw057.

Hubalek V, X Wu, A Eiler, M Buck, C Heim , M Dopson, S Bertilsson & D Ionescu (2016) Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield. ISME J 10: 2447-2458.

Bunse C, D Lundin, CMG Karlsson, N Akram, M Vila-Costa, J Palovaara, L Svensson, K Holmfeldt, JM González, E Calvo, C Pelejero, C Marrasé, M Dopson, JM Gasol & J Pinhassi (2016) Response of marine bacterioplankton pH homeostasis gene expression to elevated CO2. Nature Clim Change 6: 483–487. doi:10.1038/nclimate2914.

Wu X, K Holmfeldt, V Hubalek, D Lundin, M Åström, S Bertilsson & M Dopson (2016) Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations. ISME J 10: 1192-1203.

2015

Broman E, M Brüsin, M Dopson & S Hylander (2015) Oxygenation of anoxic sediments triggers hatching of zooplankton eggs. Proc Royal Soc B 282, doi: 10.1098/rspb.2015.2025.

Esparza M, E Jedlicki, M Dopson & DS Holmes (2015) Expression and activity of the Calvin-Benson-Bassham cycle transcriptional regulator CbbR from Acidithiobacillus ferrooxidans in Ralstonia eutropha. FEMS Microbiol Lett 362: doi: 10.1093/femsle/fnv108.

Wu X, P Sten, S Engblom, P Nowak, P Österholm & M Dopson (2015) Impact of mitigation strategies on acid sulfate soil chemistry and microbial community. Sci Tot Environ 526: 215-221.

Liljeqvist M, FJ Ossandon, C Gonzalez, S Rajan, A Stell, J Valdes, DS Holmes & M Dopson (2015) Metagenomic analysis reveals adaptations to a psychrotrophic lifestyle in a low temperature acid mine drainage stream. FEMS Microbiol Ecol In-press: http://dx.doi.org/10.1093/femsec/fiv011

2014

Khoshkhoo M, M Dopson, Å Sandström (2014) Chalcopyrite leaching and bioleaching: An XPS study to characterize the nature of hindered dissolution. Hydrometallurgy 149: 220–227.

González C, M Yanquepe, J-P Cardenas, J Valdes, R Quatrini, DS Holmes & M Dopson (2014) Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis. Res Microbiol 165: 726-734.

Khoshkhoo M, M Dopson, A Shchukarev & Å Sandström (2014) Electrochemical simulation of redox potential development in bioleaching of a pyritic chalcopyrite concentrate. Hydrometallurgy 144-145: 7-14.

2013

Acuña LG, PA Covarrubias; JP Cárdenas, JJ Haristoy, R Flores, H Nuñez, G Riadi, S Amir, J Valdés, M Dopson, DE Rawlings, JF Banfield, DS Holmes & R Quatrini (2013) Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus. PLoS ONE 8: e78237. doi:10.1371/journal.pone.0078237.

Mangold S, V rao Jonna & M Dopson (2013) Response of Acidithiobacillus caldus towards suboptimal pH conditions. Extremophiles 17: 689-696.

Wu X, ZL Wong, P Sten, S Engblom, P Österholm & M Dopson (2013) Microbial community potentially responsible for acid and metal release from an Ostrobothnian acid sulfate soil. FEMS Microbiol Ecol 84: 555-563.

Osorio H, S Mangold, Y Denis, I Ňancucheo, DB Johnson, V Bonnefoy, M Dopson & DS Holmes (2013) Anaerobic sulfur metabolism coupled to dissimilatory iron reduction in the extremophile Acidithiobacillus ferrooxidans. Appl Environ Microbiol 79: In-press.

Liljeqvist M, OI. Rzhepishevska & M Dopson (2013) Gene identification and substrate regulation provides insights into sulfur accumulation during bioleaching with the psychrotolerant acidophile Acidithiobacillus ferrivorans. Appl Environ Microbiol 79: 951-957.

Mangold S, J Potrykus, E Björn, L Lövgren & M Dopson (2013) Extreme zinc tolerance in acidophilic microorganisms from the bacterial and archaeal domains. Extremophiles 17:75-85.

2012

Zammit CM, S Mangold, V rao Jonna , LA Mutch, HR Watling, M Dopson & ELJ Watkin (2012) Bioleaching in brackish waters-effect of chloride ions on the acidophile population and proteomes of model species. Appl Microbiol Biotechnol 93:319-329.

2011

Valdes J, F Ossandon, R Quatrini, M Dopson & DS Holmes (2011) Draft genome sequence of the extremely acidophilic biomining bacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus. J Bacteriol 193: 7003-7004.

Liljeqvist M, J Valdes, DS Holmes & M Dopson (2011) Draft genome of the psychrotolerant acidophile Acidithiobacillus ferrivorans SS3. J Bacteriol: 193: 4304-4305.

Liljeqvist M, J-E Sundkvist, A Saleh & M Dopson (2011) Low temperature removal of inorganic sulfur compounds from mining process waters. Biotechnol Bioengin: 108:1251-1259.

Potrykus J, V rao Jonna & M Dopson (2011) Iron homeostasis and responses to iron limitation in extreme acidophiles from the Ferroplasma genus. Proteomics 11: 52–63.

2010

Baker-Austin C, J Potrykus, M Wexler, PL Bond & M Dopson (2010) Biofilm development in the extremely acidophilic archaeon 'Ferroplasma acidarmanus' Fer1 does not require known signaling systems. Extremophiles 14: 485-491.

Bijmans MFM, E de Vries, C-H Yang, CJN Buisman, PNL Lens & M Dopson (2010) Sulfate reduction at pH 4.0 for treatment of process and wastewaters. Biotechnol Prog 26: 1029-1037.

Gahan CS, J-E Sundkvist, M Dopson, Å Sandström (2010) Effect of chloride on ferrous iron oxidation by a Leptospirillum ferriphilum-dominated chemostat culture. Biotechnol Bioengin 106: 422-431.

2009

Kupka D, M Liljeqvist, P Nurmi, JA Puhakka, OH Tuovinen & M Dopson (2009) Oxidation of elemental sulfur, tetrathionate, and ferrous iron by the psychrotolerant Acidithiobacillus strain SS3. Res Microbiol 160: 767-774.

Dar SA, MFM Bijmans, IJT Dinkla, B Geurkink, PNL Lens & M Dopson (2009) Population dynamics of a single stage sulfidogenic bioreactor treating synthetic zinc- containing waste streams. Microbial Ecol 58: 529-537.

Valdes J, R Quatrini, K Hallberg, M Dopson, PD Valenzuela & DS Holmes (2009) Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the Acidithiobacillus genus. J Bacteriol 191: 5877–5878.

Bijmans MFM, M Dopson, TWT Peeters, PNL Lens & CJN Buisman (2009) Sulfate reduction at pH 5 in a high-rate membrane bioreactor: Reactor performance and microbial community analyses. J Microbiol Biotechnol 19: 698-708.

Dopson M, L Lövgren & D Boström (2009) Silicate mineral dissolution in the presence of acidophilic microorganisms - Implications for heap bioleaching. Hydrometallurgy 96: 288 - 293.

Bijmans MFM, P-J van Helvoort, SA Dar, M Dopson, PNL Lens & CJN Buisman (2009) Selective recovery of nickel from a nickel-iron solution using microbial sulfate reduction in a gas-lift bioreactor. Water Res 43: 853-861.

2008

Bijmans MFM, M Dopson, F Ennin, PNL Lens & CJN Buisman (2008) Effect of sulfide removal on sulfate reduction at pH 5 in a hydrogen fed gas-lift bioreactor. J Microbiol Biotechnol 18: 1809-1818.

Dopson M, A-K Halinen, N Rahunen, D Boström, J-E Sundkvist, M Riekkola-Vanhanen, AH Kaksonen & JA Puhakka (2008) Silicate mineral dissolution during heap bioleaching: Implications for heap bioleaching. Biotechnol Bioengin 99: 811-820.

Nicomrat D, WA Dick, M Dopson & OH Tuovinen (2008) Bacterial phylogenetic diversity in a constructed wetland system treating acid coal mine drainage. Soil Biol Biochem 40: 312-321.

2007

Rzhepishevska OI, J Valdés, L Marcinkeviciene, CA Gallardo, R Meskys, V Bonnefoy, DS Holmes & M Dopson (2007) Regulation of a novel Acidithiobacillus caldus gene cluster involved in reduced inorganic sulfur compound metabolism. Appl Environ Microbiol 73: 7367–7372.

Kupka D, OI Rzhepishevska, M Dopson, EB Lindström, OV Karnachuk & OH Tuovinen (2007) Bacterial oxidation of ferrous iron at low temperatures. Biotechnol Bioengin 97: 1470-1478. (In conjunction with this article is a spotlight in the same issue: Boreal isolates of iron-oxidizing bacteria provide insights to low-temperature bioleaching p. vii).

Dopson M, A-K Halinen, N Rahunen, B Özkaya, E Sahinkaya, AH Kaksonen, EB Lindström & JA Puhakka (2007) Mineral and iron oxidation at low temperatures by pure and mixed cultures of acidophilic microorganisms. Biotechnol Bioengin 97: 1205-1215.

Baker-Austin C, Dopson M, M Wexler, RG Sawers, A Stemmler, BP Rosen & PL Bond (2007) Extreme arsenic resistance by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1. Extremophiles 11: 425-434. Dopson and Baker-Austin contributed equally to this paper.

Dopson M, C Baker-Austin & PL Bond (2007) Towards determining details of anaerobic growth coupled to iron reduction by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1. Extremophiles 11: 159-168.

2006

Dopson M, J-E Sundkvist & EB Lindström (2006) Toxicity of metal extraction and flotation chemicals to Sulfolobus metallicus and chalcopyrite bioleaching. Hydrometallurgy 81: 205-213.

2005

Rzhepishevska OI, EB Lindström, OH Tuovinen & M Dopson (2005) Bioleaching of sulfidic tailing samples with a novel, vacuum-positive pressure driven bioreactor. Biotechnol Bioengin 92: 559-567.

Dopson M, C Baker-Austin & PL Bond (2005) Analysis of differential protein expression during growth states of Ferroplasma strains and insights into electron transport for iron oxidation. Microbiology 151: 4127-4137.

Baker-Austin C, M Dopson, M Wexler, G Sawers & PL Bond (2005) Molecular insight into extreme copper resistance in the extremophilic archaeon "Ferroplasma acidarmanus" Fer1. Microbiology 151: 2637-2646.

Morales TA, M Dopson, R Athar & R Herbert (2005) Analysis of bacterial diversity in acidic pond water and compost after treatment of artificial acid mine drainage for metal removal. Biotechnol Bioengin 90: 543-551.

2004

Dopson M & EB Lindström (2004) Analysis of community composition during moderately thermophilic bioleaching of pyrite, arsenical pyrite and chalcopyrite. Microbial Ecol 48: 19-28.

Dopson M, C Baker-Austin & PL Bond (2004) First use of 2-dimensional polyacrylamide gel electrophoresis for classification of microorganisms. J Microbiol Methods 58: 297-302.

Dopson M, C Baker-Austin, A Hind, JP Bowman & PL Bond (2004) Characterization of Ferroplasma isolates and Ferroplasma acidarmanus sp. nov., extreme acidophiles from acid mine drainage and industrial bioleaching environments. Appl Environ Microbiol 70: 2079-2088.

2002

Dopson M, EB Lindström & KB Hallberg (2002) ATP generation during reduced inorganic sulfur compound oxidation by Acidithiobacillus caldus is exclusively due to electron transport phosphorylation. Extremophiles 6: 123-129.

2001

Dopson M, EB Lindström & KB Hallberg (2001) Chromosomally encoded arsenical resistance of the moderately thermophilic acidophile Acidithiobacillus caldus. Extremophiles 5: 247-255.

1999

Dopson M & EB Lindström (1999) Potential role of Thiobacillus caldus in arsenopyrite bioleaching. Appl Environ Microbiol 65: 36-40.

1996

Hallberg KB, M Dopson & EB Lindström (1996) Arsenic toxicity is not due to a direct effect on the oxidation of reduced inorganic sulfur compounds by Thiobacillus caldus. FEMS Microbiol Lett 145: 409-414.

Hallberg KB, M Dopson & EB Lindström (1996) Reduced sulfur compound oxidation by Thiobacillus caldus. J Bacteriol 178: 6-11. Hallberg and Dopson contributed equally to this paper.

2016

Dopson M, G Ni & THJA Sleutels (2016) Possibilities for extremophilic microorganisms in bioelectrochemical systems. FEMS Microbiol Rev 40: 164–181.

2015

Dopson M, G Ni & THJA Sleutels (2015) Possibilities for extremophilic microorganisms in bioelectrochemical systems. FEMS Microbiol Rev In-press: doi: 10.1093/femsre/fuv044.

2014

Dopson M & Holmes DS (2014) Metal resistance in acidophilic microorganisms and its significance for biotechnologies. Appl Microbiol Biotechnol 98: 8133-8144.

Dopson M, FJ Ossandon, L Lövgren & DS Holmes (2014) Metal resistance or tolerance? Acidophiles confront high metal loads via both abiotic and biotic mechanisms. Front Microbio 5: doi: 10.3389/fmicb.2014.00157.

2012

Dopson M & Johnson DB (2012) Biodiversity, metabolism and applications of acidophilic sulfur- metabolizing micro-organisms. Environ Microbiol: 14: 2620–2631.

2009

Slonczewski JL, M Fujisawa, M Dopson & TA Krulwich (2009) Cytoplasmic pH measurement and homeostasis in bacteria and archaea. Adv Microb Physiol 55: 1-79.

2007

Baker-Austin C & M Dopson (2007) Life in acid: pH homeostasis in acidophiles. Trends Microbiol 15: 165-171.

2003

Dopson M, C Baker-Austin, PR Koppineedi & PL Bond (2003) Growth in sulfidic mineral environments: Metal resistance mechanisms in acidophilic microorganisms. Microbiology 149: 1959-1970.

2016

Dopson M (2016) Physiological and phylogenetic diversity of acidophilic bacteria. In Acidophiles: life in extremely acidic environments. Johnson DB & Qutrini R (eds.) Caister Academic Press, UK. (ISBN: 978-1-910190-33-3) pp. 79 - 92.

2012

Dopson M (2012) Physiological adaptations and biotechnological applications of acidophiles. In: Extremophiles: Microbiology and Biotechnology. Anitori R (Ed.). Horizon Press (ISBN: 978-1-904455-98-1) pp. 265-294.

2008

Kaksonen AH, M Dopson, O Karnachuk, OH Tuovinen & JA Puhakka (2008) Biological iron oxidation and sulfate reduction in the treatment of acid mine drainage at low temperatures. In: Psychrophiles: from biodiversity to biotechnology. Margesin R, F Schinner, J-C Marx & C Gerday (Eds.). Springer-Verlag (ISBN: 978-3-540-74334-7).