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  • 51.
    Bonnedahl, Jonas
    et al.
    Uppsala University ; Kalmar County Hospital.
    Drobni, M
    Gauthier-Clerc, M
    Hernandez, Jorge
    Kalmar County Hospital.
    Granholm, S
    Kayser, Y
    Melhus, Å
    Kahlmeter, G
    Waldenström, Jonas
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Johansson, A
    Olsen, Björn
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Dissemination of Escherichia coli with CTX-M Type ESBL between Humans and Yellow-Legged Gulls in the South of France2009In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 4, no Article number: e5958Article in journal (Refereed)
    Abstract [en]

     Extended Spectrum beta-Lactamase (ESBL) producing Enterobacteriaceae started to appear in the 1980s, and have since emerged as some of the most significant hospital-acquired infections with Escherichia coli and Klebsiella being main players. More than 100 different ESBL types have been described, the most widespread being the CTX-M beta-lactamase enzymes (bla(CTX-M) genes). This study focuses on the zoonotic dissemination of ESBL bacteria, mainly CTX-M type, in the southern coastal region of France. We found that the level of general antibiotic resistance in single randomly selected E. coli isolates from wild Yellow-legged Gulls in France was high. Nearly half the isolates (47,1%) carried resistance to one or more antibiotics (in a panel of six antibiotics), and resistance to tetracycline, ampicillin and streptomycin was most widespread. In an ESBL selective screen, 9,4% of the gulls carried ESBL producing bacteria and notably, 6% of the gulls carried bacteria harboring CTX-M-1 group of ESBL enzymes, a recently introduced and yet the most common clinical CTX-M group in France. Multi locus sequence type and phylogenetic group designations were established for the ESBL isolates, revealing that birds and humans share E. coli populations. Several ESBL producing E. coli isolated from birds were identical to or clustered with isolates with human origin. Hence, wild birds pick up E. coli of human origin, and with human resistance traits, and may accordingly also act as an environmental reservoir and melting pot of bacterial resistance with a potential to re-infect human populations.

  • 52.
    Bonnedahl, Jonas
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Kalmar County Hospital.
    Stedt, Johan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Waldenström, Jonas
    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.
    Drobni, Mirva
    Uppsala University.
    Olsen, Björn
    Uppsala University.
    Comparison of Extended-Spectrum beta-Lactamase (ESBL) CTX-M Genotypes in Franklin Gulls from Canada and Chile2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 10, article id e0141315Article in journal (Refereed)
    Abstract [en]

    Migratory birds have been suggested to contribute to long-distance dispersal of antimicrobial resistant bacteria, but tests of this hypothesis are lacking. In this study we determined resistance profiles and genotypes of ESBL-producing bacteria in randomly selected Escherichia coli from Franklin's gulls (Leucophaeus pipixcan) at breeding sites in Canada and compared with similar data from the gulls' wintering grounds in Chile. Resistant E. coli phenotypes were common, most notably to ampicillin (30.1%) and cefadroxil (15.1%). Furthermore, 17.0% of the gulls in Canada carried ESBL producing bacteria, which is higher than reported from human datasets from the same country. However, compared to gulls sampled in Chile (30.1%) the prevalence of ESBL was much lower. The dominant ESBL variants in Canada were bla(CTX-M-14) and bla(CTX-M-15) and differed in proportions to the data from Chile. We hypothesize that the observed differences in ESBL variants are more likely linked to recent exposure to bacteria from anthropogenic sources, suggesting high local dissemination of resistant bacteria both at breeding and non-breeding times rather than a significant trans-hemispheric exchange through migrating birds.

  • 53.
    Boström, Kjärstin H.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Nitrogen fixation among marine bacterioplankton2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    While bacterioplankton indisputably control vital biogeochemical paths in the cycling of carbon and nutrients in the world’s oceans, our knowledge about the functional and genetic diversity of bacterioplankton communities is negligible. In this thesis, molecular and more traditional microbiological methods were used to study the specific function of N2-fixation and in a general sense diversity of marine bacterioplankton species.

    Most oceans are nitrogen limited and, therefore, adaptive to bacterioplankton capable of N2-fixation. Recent studies have found nifH genes (coding for the nitrogenase enzyme) related to diverse heterotrophic bacteria in oceanic seawater samples indicating that, along with cyanobacteria, also heterotrophic bacteria benefit from N2-fixation. Here, molecular and cultivation methods were used to examine diazotrophic bacterioplankton in the Baltic Sea. We successfully isolated heterotrophic N2-fixing bacteria belonging to the γ-proteobacterial class by means of low-nitrogen plates and semi-solid diazotrophic medium tubes. The isolates required low-O2 conditions for N2-fixation. Using Real-time PCR it was found that heterotrophic bacterioplankton carrying the nifH gene was abundant (3 x 104 nifH gene copies L seawater-1) at locations in the Southwest Baltic proper.

    With the aim to identify the main N2-fixing organisms in Baltic Proper surface waters, a clone library of nifH gene transcripts (RNA) was generated. Clone inserts were exclusively related to Aphanizomenon sp. and Nodularia sp. Using quantitative real-time PCR it was found that the nifH gene expression from Nodularia sp. was highly variable between stations in the Baltic Proper but was 10-fold higher during mid summer relative to early summer and fall. A diel study showed a 4-fold increase in Nodularia transcript concentrations at early to mid day relative to rest of the day. Real-time PCR was found to be a powerful and highly sensitive method for measuring gene expression.

    Since nucleic acids are a prerequisite for molecular analyses of bacterioplankton dynamics a protocol to extract DNA from seawater samples was developed with the aim to maximize the yield of high-quality DNA. Each step in the protocol was important for the efficiency of extraction. The obtained extraction efficiencies were up to 92% for seawater samples and up to 96% for isolates. The protocol provides a guideline for DNA extraction from seawater samples for other studies.

    In a global sampling campaign (9 locations from polar, tropical and temperate regions) we sampled DNA from surface water and constructed 16S rRNA gene libraries to investigate diversity and biogeography of bacterioplankton. Approx. 80% of the sequences found were similar to sequences already deposited in GenBank, indicating that a large fraction of the marine bacterioplankton already has been sampled, which in turn suggests a limited global bacterioplankton diversity.

    This thesis have improved our knowledge about the composition and nifH gene expression of the diazotrophic bacterioplankton community in the Baltic Sea and contribute significantly to the discussion on global marine bacterioplankton diversity and biogeography.

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  • 54.
    Boström, Kjärstin H.
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Reimann, Lasse
    Kühl, Michael
    Hagström, Åke
    Isolation and gene quantification of heterotrophic N2-fixing bacterioplankton in the Baltic Sea2007In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 9, no 1, p. 152-164Article in journal (Refereed)
  • 55.
    Boström, Kjärstin H.
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Riemann, Lasse
    Zweifel, Ulla Li
    Hagström, Åke
    Nodularia sp. nifH gene transcripts in the Baltic Sea proper2007In: Journal of Plankton Research, ISSN 0142-7873, E-ISSN 1464-3774, Vol. 29, no 4, p. 391-399Article in journal (Refereed)
  • 56.
    Boström, Kjärstin
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Simu, Karin
    Hagström, Åke
    Riemann, Lasse
    Optimization of DNA extraction for quantitative marine bacterioplankton community analysis2004In: Limnology and oceanography: methods, Vol. 2, p. 365-373Article in journal (Refereed)
  • 57.
    Brindefalk, Bjorn
    et al.
    Stockholm University.
    Ekman, Martin
    Stockholm University.
    Ininbergs, Karolina
    Stockholm University.
    Dupont, Christopher L.
    J Craig Venter Inst, USA.
    Yooseph, Shibu
    J Craig Venter Inst, USA.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bergman, Birgitta
    Stockholm University.
    Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, p. 4442-4455Article in journal (Refereed)
    Abstract [en]

    Rhodopsins are light-driven ion-pumping membrane proteins found in many organisms and are proposed to be of global importance for oceanic microbial energy generation. Several studies have focused on marine environments, with less exploration of rhodopsins in brackish waters. We investigated microbial rhodopsins in the Baltic Sea using size-fractionated metagenomic and metatranscriptomic datasets collected along a salinity gradient spanning from similar to 0 to 35 PSU. The normalised genomic abundance of rhodopsins in Bacteria, as well as rhodopsin gene expression, was highest in the smallest size fraction (0.1-0.8 mu m), relative to the medium (0.8-3.0 mu m) and large (> 3.0 mu m) size fractions. The abundance of rhodopsins in the two smaller size fractions displayed a positive correlation with salinity. Proteobacteria and Bacteroidetes rhodopsins were the most abundant while Actinobacteria rhodopsins, or actinorhodopsins, were common at lower salinities. Phylogenetic analysis indicated that rhodopsins have adapted independently to the marine-brackish transition on multiple occasions, giving rise to green light-adapted variants from ancestral blue light-adapted ones. A notable diversity of viral-like rhodopsins was also detected in the dataset and potentially linked with eukaryotic phytoplankton blooms. Finally, a new clade of likely proton-pumping rhodopsin with non-canonical amino acids in the spectral tuning and proton accepting site was identified.

  • 58. Brojer, Caroline
    et al.
    Jarhult, Josef D.
    Muradrasoli, Shaman
    Soderstrom, Hanna
    Olsen, Björn
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Gavier-Widen, Dolores
    Pathobiology and virus shedding of low-pathogenic avian influenza virus (A/H1N1) infection in mallards exposed to oseltamivir2013In: Journal of Wildlife Diseases, ISSN 0090-3558, E-ISSN 1943-3700, Vol. 49, no 1, p. 103-113Article in journal (Refereed)
    Abstract [en]

    Low-pathogenic avian influenza (LPAI) viruses in wild birds are important as they can constitute the basis for the development of highly pathogenic avian influenza viruses or form part of human-adapted strains with pandemic potential. However, the pathogenesis of LPAI viruses is not well characterized in dabbling ducks, one of the natural reservoirs of LPAI viruses. Between 21 September 2009 and 21 December 2009, we used real-time reverse transcriptase polymerase chain reaction (q-PCR), histopathology, and immunohistochemistry (IHC) to study Mallards (Anas platyrhynchos) infected with an influenza A/H1N1 virus isolated from a wild Mallard in Sweden. The ducks were either inoculated intraesophageally ("artificial infection") or infected by virus shed by other ducks in the experiment ("contact infection"). The ducks were subjected to three low concentrations (80 ng/L, 1 mu g/L, and 80 mu g/L) of the active metabolite of oseltamivir (Tamiflu (R)), oseltamivir carboxylate (OC), which resulted in the development of the viral resistance mutation H274Y at 1 and 80 mu g/L. The LPAI virus infection was localized to the intestinal tract and cloacal bursa except in one Mallard. The exception was a duck euthanized 1 day postinoculation, whose infection was located solely in the lung, possibly due to intratracheal deposition of virus. The intestinal infection was characterized by occasional degenerating cells in the lamina propria and presence of viral antigen as detected by IHC, as well as positive q-PCR performed on samples from feces and intestinal contents. Histopathologic changes, IHC positivity, and viral shedding all indicated that the infection peaked early, around 2 days postinfection. Furthermore, more viral antigen and viral RNA were detected with IHC and q-PCR in the proximal parts early in the infection. There was no obvious difference in the course of the infection in artificial versus contact infection, when the level of OC was increased from 80 ng/L to 1 mu g/L (based on IHC and q-PCR), when the level of OC was increased to 80 mu/L, or when the resistance mutation H274Y developed (based on q-PCR).

  • 59.
    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.

  • 60.
    Broman, Elias
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Stockholm University, Sweden.
    Asmala, Eero
    Univ Helsinki, Finland.
    Carstensen, Jacob
    Aarhus Univ, 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.
    Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter2019In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, p. 1-15, article id 2579Article in journal (Refereed)
    Abstract [en]

    Coastal zones are important transitional areas between the land and sea, where both terrestrial and phytoplankton supplied dissolved organic matter (DOM) are respired or transformed. As climate change is expected to increase river discharge and water temperatures, DOM from both allochthonous and autochthonous sources is projected to increase. As these transformations are largely regulated by bacteria, we analyzed microbial community structure data in relation to a 6-month long time-series dataset of DOM characteristics from Roskilde Fjord and adjacent streams, Denmark. The results showed that the microbial community composition in the outer estuary (closer to the sea) was largely associated with salinity and nutrients, while the inner estuary formed two clusters linked to either nutrients plus allochthonous DOM or autochthonous DOM characteristics. In contrast, the microbial community composition in the streams was found to be mainly associated with allochthonous DOM characteristics. A general pattern across the land-to-sea interface was that Betaproteobacteria were strongly associated with humic-like DOM [operational taxonomic units (OTUs) belonging to family Comamonadaceae], while distinct populations were instead associated with nutrients or abiotic variables such as temperature (Cyanobacteria genus Synechococcus) and salinity (Actinobacteria family Microbacteriaceae). Furthermore, there was a stark shift in the relative abundance of OTUs between stream and marine stations. This indicates that as DOM travels through the land-to-sea interface, different bacterial guilds continuously degrade it.

  • 61.
    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.

  • 62.
    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.

  • 63.
    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

  • 64.
    Buetti-Dinh, Antoine
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. 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.
    El Hajjami, Mohamed
    QNLM, China.
    Delogu, Francesco
    Norwegian University of Life Sciences, Norway.
    Ilie, Olga
    Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    Bellenberg, Sören
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wilmes, Paul
    University of Luxembourg, Luxembourg.
    Poetsch, Ansgar
    Ruhr University Bochum, Germany;QNLM, China;Ocean University of China, China.
    Sand, Wolfgang
    University Duisburg-Essen, Germany;Donghua University, China;3Mining Academy and Technical University Freiberg, Germany.
    Vera, Mario
    Pontificia Universidad Católica de Chile, Chile.
    Pivkin, Igor V.
    Università della Svizzera italiana, Switzerland;Swiss Institute of Bioinformatics, Switzerland.
    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.
    Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations2020In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 21, no 1, p. 1-15, article id 23Article in journal (Refereed)
    Abstract [en]

    Background: Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data, such as RNAseq or mass spectrometry-based proteomics data, through computational methods. This approach allows to identify signalling pathways involved in specific biological functions. The ability to infer causality in gene regulatory networks, in addition to correlation, is crucial for several modelling approaches and allows targeted control in biotechnology applications. Methods: We performed simulations according to the approximate Bayesian computation method, where the core model consisted of a steady-state simulation algorithm used to study gene regulatory networks in systems for which a limited level of details is available. The simulations outcome was compared to experimentally measured transcriptomics and proteomics data through approximate Bayesian computation. Results: The structure of small gene regulatory networks responsible for the regulation of biological functions involved in biomining were inferred from multi OMICs data of mixed bacterial cultures. Several causal inter- and intraspecies interactions were inferred between genes coding for proteins involved in the biomining process, such as heavy metal transport, DNA damage, replication and repair, and membrane biogenesis. The method also provided indications for the role of several uncharacterized proteins by the inferred connection in their network context. Conclusions: The combination of fast algorithms with high-performance computing allowed the simulation of a multitude of gene regulatory networks and their comparison to experimentally measured OMICs data through approximate Bayesian computation, enabling the probabilistic inference of causality in gene regulatory networks of a multispecies bacterial system involved in biomining without need of single-cell or multiple perturbation experiments. This information can be used to influence biological functions and control specific processes in biotechnology applications.

  • 65.
    Bunse, Carina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bacterioplankton in the light of seasonality and environmental drivers2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Bacterioplankton are keystone organisms in marine ecosystems. They are important for element cycles, by transforming dissolved organic carbon and other nutrients. Bacterioplankton community composition and productivity rates change in surface waters over spatial and temporal scales. Yet, many underlying biological processes determining when, why and how bacterioplankton react to changes in environmental conditions are poorly understood. Here, I used experiments with model bacteria and natural assemblages as well as field studies to determine molecular, physiological and ecological responses allowing marine bacteria to adapt to their environment.

    Experiments with the flavobacterium Dokdonia sp. MED134 aimed to determine how the metabolism of bacteria is influenced by light and different organic matter. Under light exposure, Dokdonia sp. MED134 expressed proteorhodopsin and adjusted its metabolism to use resources more efficiently when growing with lower-quality organic matter. Similar expression patterns were found in oceanic datasets, implying a global importance of photoheterotrophic metabolisms for the ecology of bacterioplankton.

    Further, I investigated how the composition and physiology of bacterial assemblages are affected by elevated CO2 concentrations and inorganic nutrients. In a large-scale experiment, bacterioplankton could keep productivity and community structure unaltered by adapting the gene expression under CO2 stress. To maintain pH homeostasis, bacteria induced higher expression of genes related to respiration, membrane transport and light acquisition under low-nutrient conditions. Under high-nutrient conditions with phytoplankton blooms, such regulatory mechanisms were not necessary. These findings indicate that open ocean systems are more vulnerable to ocean acidification than coastal waters.

    Lastly, I used field studies to resolve how bacterioplankton is influenced by environmental changes, and how this leads to seasonal succession of marine bacteria. Using high frequency sampling over three years, we uncovered notable variability both between and within years in several biological features that rapidly changed over short time scales. These included potential phytoplankton-bacteria linkages, substrate uptake rates, and shifts in bacterial community structure. Thus, high resolution time series can provide important insights into the mechanisms controlling microbial communities.

    Overall, this thesis highlights the advantages of combining molecular and traditional oceanographic methodological approaches to study ecosystems at high resolution for improving our understanding of the physiology and ecology of microbial communities and, ultimately, how they influence biogeochemical processes.

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    Errata
  • 66.
    Bunse, Carina
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bertos-Fortis, Mireia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sassenhagen, Ingrid
    Lund University.
    Sildever, Sirje
    Tallinn University of Technology, Estonia.
    Sjöqvist, Conny
    Marine Research Centre, Finland;Åbo Akademi University, Finland.
    Godhe, Anna
    University of Gothenburg.
    Gross, Susanna
    University of Gothenburg.
    Kremp, Anke
    Marine Research Centre, Finland.
    Lips, Inga
    Tallinn University of Technology, Estonia.
    Lundholm, Nina
    University of Copenhagen, Denmark.
    Rengefors, Karin
    Lund University.
    Sefbom, Josefin
    University of Gothenburg.
    Pinhassi, Jarone
    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.
    Spatio-Temporal Interdependence of Bacteria and Phytoplankton during a Baltic Sea Spring Bloom2016In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, article id 517Article in journal (Refereed)
    Abstract [en]

    In temperate systems, phytoplankton spring blooms deplete inorganic nutrients and are major sources of organic matter for the microbial loop. In response to phytoplankton exudates and environmental factors, heterotrophic microbial communities are highly dynamic and change their abundance and composition both on spatial and temporal scales. Yet, most of our understanding about these processes comes from laboratory model organism studies, mesocosm experiments or single temporal transects. Spatial -temporal studies examining interactions of phytoplankton blooms and bacterioplankton community composition and function, though being highly informative, are scarce. In this study, pelagic microbial community dynamics (bacteria and phytoplankton) and environmental variables were monitored during a spring bloom across the Baltic Proper (two cruises between North Germany to Gulf of Finland). To test to what extent bacterioplankton community composition relates to the spring bloom, we used next generation amplicon sequencing of the 16S rRNA gene, phytoplankton diversity analysis based on microscopy counts and population genotyping of the dominating diatom Skeletonema rnarinoi. Several phytoplankton bloom related and environmental variables were identified to influence bacterial community composition. Members of Bacteroidetes and Alphaproteobacteria dominated the bacterial community composition but the bacterial groups showed no apparent correlation with direct bloom related variables. The less abundant bacterial phyla Actinobacteria, Planctomycetes, and Verrucomicrobia, on the other hand, were strongly associated with phytoplankton biomass, diatom:dinoflagellate ratio, and colored dissolved organic matter (cDOM). Many bacterial operational taxonomic units (OTUs) showed high niche specificities. For example, particular Bacteroidetes OTUs were associated with two distinct genetic clusters of S. marinoi. Our study revealed the complexity of interactions of bacterial taxa with inter- and intraspecific genetic variation in phytoplankton. Overall, our findings imply that biotic and abiotic factors during spring bloom influence bacterial community dynamics in a hierarchical manner.

  • 67.
    Bunse, Carina
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Carl von Ossietzky Univ Oldenburg, Germany.
    Israelsson, Stina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Vienna, Austria.
    Bertos-Fortis, Mireia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Fridolfsson, Emil
    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.
    Lindehoff, Elin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Swedish Meteorological & Hydrological Institute.
    Martínez-García, Sandra
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Vigo, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    High Frequency Multi-Year Variability in Baltic Sea Microbial Plankton Stocks and Activities2019In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 3296Article in journal (Refereed)
    Abstract [en]

    Marine bacterioplankton are essential in global nutrient cycling and organic matter turnover. Time-series analyses, often at monthly sampling frequencies, have established the paramount role of abiotic and biotic variables in structuring bacterioplankton communities and productivities. However, fine-scale seasonal microbial activities, and underlying biological principles, are not fully understood. We report results from four consecutive years of high-frequency time-series sampling in the Baltic Proper. Pronounced temporal dynamics in most investigated microbial variables were observed, including bacterial heterotrophic production, plankton biomass, extracellular enzyme activities, substrate uptake rate constants of glucose, pyruvate, acetate, amino acids, and leucine, as well as nutrient limitation bioassays. Spring blooms consisting of diatoms and dinoflagellates were followed by elevated bacterial heterotrophic production and abundances. During summer, bacterial productivity estimates increased even further, coinciding with an initial cyanobacterial bloom in early July. However, bacterial abundances only increased following a second cyanobacterial bloom, peaking in August. Uptake rate constants for the different measured carbon compounds varied seasonally and inter-annually and were highly correlated to bacterial productivity estimates, temperature, and cyanobacterial abundances. Further, we detected nutrient limitation in response to environmental conditions in a multitude of microbial variables, such as elevated productivities in nutrient bioassays, changes in enzymatic activities, or substrate preferences. Variations among biotic variables often occurred on time scales of days to a few weeks, yet often spanning several sampling occasions. Such dynamics might not have been captured by sampling at monthly intervals, as compared to more predictable transitions in abiotic variables such as temperature or nutrient concentrations. Our study indicates that high resolution analyses of microbial biomass and productivity parameters can help out in the development of biogeochemical and food web models disentangling the microbial black box.

  • 68.
    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.

  • 69.
    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.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University.
    Sjöstedt, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Israelsson, Stina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Martínez-García, Sandra
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Universidade de Vigo, Spain.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Otago, New Zealand.
    Muthusamy, Sarala Devi
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pontiller, Benjamin
    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.
    Legrand, Catherine
    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.
    Seasonality and co-occurrences of free-living Baltic Sea bacterioplanktonManuscript (preprint) (Other academic)
  • 70. Carlsson, Beatrice
    et al.
    Lindberg, A. Michael
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Rodrigues-Díaz, Jesus
    Hedlund, Kjell-Olof
    Persson, Bengt
    Svensson, Lennart
    Quasispecies dynamics and molecular evolution of human norovirus capsid P region during chronic infection2009In: Journal of General Virology, ISSN 0022-1317, E-ISSN 1465-2099, Vol. 90, no 2, p. 432-441Article in journal (Refereed)
    Abstract [en]

    In this novel study, we have for the first time identified evolutionarily conserved capsid residues in an individual chronically infected with norovirus (GGII.3). From 2000 to 2003, a total of 147 P1-1 and P2 capsid sequences were sequenced and investigated for evolutionarily conserved and functionally important residues by the evolutionary trace (ET) algorithm. The ET algorithm revealed more absolutely conserved residues (ACR) in the P1-1 domain (47/53, 88 %) as compared with the P2 domain (86/133, 64 %). The capsid P1-1 and P2 domains evolved in time-dependent manner, with a distinct break point observed between autumn/winter of year 2000 (isolates P1, P3 and P5) and spring to autumn of year 2001 (isolates P11, P13 and P15), which presumably coincided with a change of clinical symptoms. Furthermore, the ET analysis revealed a similar receptor-binding pattern as reported for Norwalk and VA387 strains, with the CS-4 and CS-5 patch (Norwalk strain) including residues 329 and 377 and residues 306 and 310, respectively, all being ACR in all partitions. Most interesting was that residues 343, 344, 345, 374, 390 and 391 of the proposed receptor A and B trisaccharide binding site (VA387 strain) within the P2 domain remained ACR in all partitions, presumably because there was no selective advantage to alter the histo blood group antigens (HBGA) receptor binding specificity. In conclusion, this study provides novel insights to the evolutionary process of norovirus during chronic infection.

  • 71.
    Cerro-Galvez, Elena
    et al.
    CSIC, IDAEA, Spain.
    Casal, Paulo
    CSIC, IDAEA, Spain.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pina, Benjamin
    CSIC, IDAEA, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dachs, Jordi
    CSIC, IDAEA, Spain.
    Vila-Costa, Maria
    CSIC, IDAEA, Spain.
    Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters2019In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, no 4, p. 1466-1481Article in journal (Refereed)
    Abstract [en]

    Thousands of semi-volatile hydrophobic organic pollutants (OPs) reach open oceans through atmospheric deposition, causing a chronic and ubiquitous pollution by anthropogenic dissolved organic carbon (ADOC). Hydrophobic ADOC accumulates in cellular lipids, inducing harmful effects on marine biota, and can be partially prone to microbial degradation. Unfortunately, their possible effects on microorganisms, key drivers of global biogeochemical cycles, remain unknown. We challenged coastal microbial communities from Ny-angstrom lesund (Arctic) and Livingston Island (Antarctica) with ADOC concentrations within the range of oceanic concentrations in 24 h. ADOC addition elicited clear transcriptional responses in multiple microbial heterotrophic metabolisms in ubiquitous groups such as Flavobacteriia, Gammaproteobacteria and SAR11. Importantly, a suite of cellular adaptations and detoxifying mechanisms, including remodelling of membrane lipids and transporters, was detected. ADOC exposure also changed the composition of microbial communities, through stimulation of rare biosphere taxa. Many of these taxa belong to recognized OPs degraders. This work shows that ADOC at environmentally relevant concentrations substantially influences marine microbial communities. Given that emissions of organic pollutants are growing during the Anthropocene, the results shown here suggest an increasing influence of ADOC on the structure of microbial communities and the biogeochemical cycles regulated by marine microbes.

  • 72.
    Christel, Stephan
    et al.
    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.
    Vera, Mario
    Unniversität Duisburg-Essen, Germany.
    Sand, Wolfgang
    Unniversität Duisburg-Essen, Germany.
    Herold, Malte
    University of Luxembourg, Luxembourg.
    Wilmes, Paul
    University of Luxembourg, Luxembourg.
    Buetti-Dinh, Antoine
    Universitá della Svizzera Italiana, Switzerland.
    Pivkin, Igor
    Universitá della Svizzera Italiana, Switzerland.
    Trötschel, Christian
    Ruhruniversität Bochum, Germany.
    Poetsch, Ansgar
    Ruhruniversität Bochum, Germany.
    Nygren, Jan
    TATAA Biocenter AB, Sweden.
    Kubista, Mikael
    TATAA Biocenter AB, Sweden.
    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.

  • 73.
    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.

  • 74.
    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'.

  • 75.
    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

  • 76.
    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.

  • 77.
    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.

  • 78.
    Cody, Alison J.
    et al.
    Univ Oxford, UK.
    McCarthy, Noel D.
    Univ Oxford,UK;Hlth Protect Agcy, UK;Univ Warwick, UK;Univ Oxford, UK.
    Bray, James E.
    Univ Oxford, UK.
    Wimalarathna, Helen M. L.
    Univ Oxford, UK.
    Colles, Frances M.
    Univ Oxford, UK.
    van Rensburg, Melissa J. Jansen
    Univ Oxford, UK.
    Dingle, Kate E.
    Univ Oxford, UK.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Maiden, Martin C. J.
    Univ Oxford, UK.
    Wild bird-associated Campylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom2015In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 7, no 5, p. 782-788Article in journal (Refereed)
    Abstract [en]

    The contribution of wild birds as a source of human campylobacteriosis was investigated in Oxfordshire, United Kingdom (UK) over a 10 year period. The probable origin of human Campylobacter jejuni genotypes, as described by multilocus sequence typing, was estimated by comparison with reference populations of isolates from farm animals and five wild bird families, using the STRUCTURE algorithm. Wild bird-attributed isolates accounted for between 476 (2.1%) and 543 (3.5%) cases annually. This proportion did not vary significantly by study year (P=0.934) but varied seasonally, with wild bird-attributed genotypes comprising a greater proportion of isolates during warmer compared with cooler months (P=0.003). The highest proportion of wild bird-attributed illness occurred in August (P<0.001), with a significantly lower proportion in November (P=0.018). Among genotypes attributed to specific groups of wild birds, seasonality was most apparent for Turdidae-attributed isolates, which were absent during cooler, winter months. This study is consistent with some wild bird species representing a persistent source of campylobacteriosis, and contributing a distinctive seasonal pattern to disease burden. If Oxfordshire is representative of the UK as a whole in this respect, these data suggest that the national burden of wild bird-attributed isolates could be in the order of 10000 annually.

  • 79.
    Comte, Jerome
    et al.
    Uppsala University ; Environm & Climate Change Canada, Canada.
    Berga, Merce
    Uppsala University ; Warnemunde IOW, Germany.
    Severin, Ina
    Uppsala University ; Leibniz Inst Freshwater Ecol & Inland Fisheries, Germany.
    Logue, Jürg Brendan
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Uppsala University.
    Lindström, Eva S.
    Uppsala University.
    Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 6, p. 2391-2404Article in journal (Refereed)
    Abstract [en]

    The diversity and composition of lake bacterial communities are driven by the interplay between local contemporary environmental conditions and dispersal of cells from the surroundings, i.e. the metacommunity. Still, a conceptual understanding of the relative importance of the two types of factors is lacking. For instance, it is unknown which sources of dispersal are most important and under which circumstances. Here, we investigated the seasonal variation in the importance of dispersal from different sources (mixing, precipitation, surface runoff and sediment resuspension) for lake bacterioplankton community and population dynamics. For that purpose, two small forest lakes and their dispersal sources were sampled over a period of 10 months. The influence of dispersal on communities and populations was determined by 454 sequencing of the 16S rRNA gene and SourceTracker analysis. On the community level direct effects of dispersal were questionable from all sources. Instead we found that the community of the preceding sampling occasion, representing growth of resident bacteria, was of great importance. On the population level, however, dispersal of individual taxa from the inlet could be occasionally important even under low water flow. The effect of sediment resuspension and precipitation appeared small.

  • 80.
    Cornejo-Castillo, Francisco M.
    et al.
    Univ Calif Santa Cruz, USA;CSIC, Spain.
    del Carmen Munoz-Marin, Maria
    Univ Calif Santa Cruz, USA;Univ Cordoba, Spain.
    Turk-Kubo, Kendra A.
    Univ Calif Santa Cruz, USA.
    Royo-Llonch, Marta
    CSIC, Spain.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Calif Santa Cruz, USA.
    Acinas, Silvia G.
    CSIC, Spain.
    Zehr, Jonathan P.
    Univ Calif Santa Cruz, USA.
    UCYN-A3, a newly characterized open ocean sublineage of the symbiotic N2-fixing cyanobacterium Candidatus Atelocyanobacterium thalassa2019In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, no 1, p. 111-124Article in journal (Refereed)
    Abstract [en]

    The symbiotic unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is one of the most abundant and widespread nitrogen (N-2)-fixing cyanobacteria in the ocean. Although it remains uncultivated, multiple sublineages have been detected based on partial nitrogenase (nifH) gene sequences, including the four most commonly detected sublineages UCYN-A1, UCYN-A2, UCYN-A3 and UCYN-A4. However, very little is known about UCYN-A3 beyond the nifH sequences from nifH gene diversity surveys. In this study, single cell sorting, DNA sequencing, qPCR and CARD-FISH assays revealed discrepancies involving the identification of sublineages, which led to new information on the diversity of the UCYN-A symbiosis. 16S rRNA and nifH gene sequencing on single sorted cells allowed us to identify the 16S rRNA gene of the uncharacterized UCYN-A3 sublineage. We designed new CARD-FISH probes that allowed us to distinguish and observe UCYN-A2 in a coastal location (SIO Pier; San Diego) and UCYN-A3 in an open ocean location (Station ALOHA; Hawaii). Moreover, we reconstructed about 13% of the UCYN-A3 genome from Tara Oceans metagenomic data. Finally, our findings unveil the UCYN-A3 symbiosis in open ocean waters suggesting that the different UCYN-A sublineages are distributed along different size fractions of the plankton defined by the cell-size ranges of their prymnesiophyte hosts.

  • 81.
    Corso, Carlos Renato
    et al.
    University of Estadual Paulista, Brazil.
    Almeida, Erica Janaína Rodrigues
    Santos, Graziely Cristina
    Morão, Luana Galvão
    Fabris, Guilherme
    Mitter, Eduardo Kovalski
    Bioremediation of direct dyes in simulated textile effluents by a paramorphogenic form of Aspergillus oryzae2012In: Water Science and Technology, ISSN 0273-1223, E-ISSN 1996-9732, Vol. 65, no 8, p. 1490-1495Article in journal (Refereed)
    Abstract [en]

    Azo dyes are extensively used for coloring textiles, paper, food, leather, drinks, pharmaceutical products, cosmetics and inks. The textile industry consumes the largest amount of azo dyes, and it is estimated that approximately 10–15% of dyes used for coloring textiles may be lost in waste streams. Almost all azo dyes are synthetic and resist biodegradation, however, they can readily be reduced by a number of chemical and biological reducing systems. Biological treatment has advantages over physical and chemical methods due to lower costs and minimal environmental effect. This research focuses on the utilization of Aspergillus oryzae to remove some types of azo dyes from aqueous solutions. The fungus, physically induced in its paramorphogenic form (called ‘pellets’), was used in the dye biosorption studies with both non-autoclaved and autoclaved hyphae, at different pH values. The goals were the removal of dyes by biosorption and the decrease of their toxicity. The dyes used were Direct Red 23 and Direct Violet 51. Their spectral stability (325–700 nm) was analyzed at different pH values (2.50, 4.50 and 6.50). The best biosorptive pH value and the toxicity limit, (which is given by the lethal concentration (LC100), were then determined. Each dye showed the same spectrum at different pH values. The best biosorptive pH was 2.50, for both non- autoclaved and autoclaved hyphae of A. oryzae. The toxicity level of the dyes was determined using the Trimmed Spearman–Karber Method, with Daphnia similis in all bioassays. The Direct Violet 51 (LC100 400 mg · mL−1) was found to be the most toxic dye, followed by the Direct Red 23 (LC100 900 mg · mL−1). The toxicity bioassays for each dye have shown that it is possible to decrease the toxicity level to zero by adding a small quantity of biomass from A. oryzae in its paramorphogenic form. The autoclaved biomass had a higher biosorptive capacity for the dye than the non-autoclaved biomass. The results show that bioremediation occurs with A. oryzae in its paramorphogenic form, and it can be used as a biosorptive substrate for treatment of industrial waste water containing azo dyes.

  • 82.
    Craik, David
    et al.
    Univ Queensland, Inst Mol Biosci, Brisbane, Qld 4072 Australia .
    Daly, Norelle
    Univ Queensland, Inst Mol Biosci, Brisbane, Qld 4072 Australia .
    Saska, Ivana
    Univ Queensland, Inst Mol Biosci, Brisbane, Qld 4072 Australia .
    Trabi, Manuela
    Univ Queensland, Inst Mol Biosci, Brisbane, Qld 4072 Australia .
    Rosengren, Johan
    Univ Queensland, Inst Mol Biosci, Brisbane, Qld 4072 Australia .
    Structures of naturally occurring circular proteins from bacteria2003In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 185, no 14, p. 4011-21Article, review/survey (Other academic)
  • 83. Dahlbäck, B.
    et al.
    Gunnarsson, L.
    Hagström, Åke
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Mikrobiologiska aspekter på musselodling1983In: Odling av blåmusslor / [ed] Rutger Rosenberg, Lund: Signum , 1983, p. 60-67Chapter in book (Other academic)
  • 84.
    Dantoft, Widad
    et al.
    Stockholm University.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Stockholm University.
    Esfahani, Shiva Seyedoleslami
    Stockholm University.
    Engström, Ylva
    Stockholm University.
    The POU/Oct Transcription Factor Pdm1/nub Is Necessary for a Beneficial Gut Microbiota and Normal Lifespan of Drosophila2016In: Journal of Innate Immunity, ISSN 1662-811X, E-ISSN 1662-8128, Vol. 8, no 4, p. 412-426Article in journal (Refereed)
    Abstract [en]

    Maintenance of a stable gut microbial community relies on a delicate balance between immune defense and immune tolerance. We have used Drosophila to study how the microbial gut flora is affected by changes in host genetic factors and immunity. Flies with a constitutively active gut immune system, due to a mutation in the POU transcriptional regulator Pdm1/nubbin (nub) gene, had higher loads of bacteria and a more diverse taxonomic composition than controls. In addition, the microbial composition shifted considerably during the short lifespan of the nub1 mutants. This shift was characterized by a loss of relatively few OTUs (operational taxonomic units) and a remarkable increase in a large number of Acetobacter spp. and Leuconostoc spp. Treating nub1 mutant flies with antibiotics prolonged their lifetime survival by more than 100%. Immune gene expression was also persistently high in the presence of antibiotics, indicating that the early death was not a direct consequence of an overactive immune defense but rather an indirect consequence of the microbial load and composition. Thus, changes in host genotype and an inability to regulate the normal growth and composition of the gut microbiota leads to a shift in the microbial community, dysbiosis and early death.

  • 85.
    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.

  • 86. Degerman, Rickard
    et al.
    Dinasquet, Julie
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Riemann, Lasse
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    de Luna, Sara Sjostedt
    Andersson, Agneta
    Effect of resource availability on bacterial community responses to increased temperature2013In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 68, no 2, p. 131-142Article in journal (Refereed)
    Abstract [en]

    Climate change is predicted to cause higher temperatures and increased precipitation, resulting in increased inflow of nutrients to coastal waters in northern Europe. This has been assumed to increase the overall heterotrophy, including enhanced bacterial growth. However, the relative importance of temperature, resource availability and bacterial community composition for the bacterial growth response is poorly understood. In the present study, we investigated effects of increased temperature on bacterial growth in waters supplemented with different nutrient concentrations and inoculated with microbial communities from distinct seasonal periods. Seven experiments were performed in the northern Baltic Sea spanning an entire annual cycle. In each experiment, bacterioplankton were exposed to 2 temperature regimes (in situ and in situ + 4 degrees C) and 5 nutrient concentrations. Generally, elevated temperature and higher nutrient levels caused an increase in the bacterial growth rate and a shortening of the response time (lag phase). However, at the lowest nutrient concentration, bacterial growth was low at all tested temperatures, implying a stronger dependence on resource availability than on temperature for bacterial growth. Furthermore, data indicated that different bacterial assemblages had varying temperature responses and that community composition was strongly affected by the combination of high nutrient addition and high temperature. These results support the concern that climate change will promote heterotrophy in aquatic systems, where nutrient levels will increase considerably. In such environments, the bacterial community composition will change, their growth rates will increase, and their response time will be shortened compared to the present situation.

  • 87.
    del Carmen Munoz-Marin, Maria
    et al.
    Univ Calif Santa Cruz, USA;Univ Cordoba, Spain.
    Shilova, Irina N.
    Univ Calif Santa Cruz, USA;Second Genome Inc, USA.
    Shi, Tuo
    Univ Calif Santa Cruz, USA;Xiamen Univ, Peoples Republic of China.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Calif Santa Cruz, USA.
    Maria Cabello, Ana
    Univ Calif Santa Cruz, USA.
    Zehr, Jonathan P.
    Univ Calif Santa Cruz, USA.
    The Transcriptional Cycle Is Suited to Daytime N2 Fixation in the Unicellular Cyanobacterium “Candidatus Atelocyanobacterium thalassa” (UCYN-A)2019In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 10, no 1, p. 1-17, article id e02495-18Article in journal (Refereed)
    Abstract [en]

    Symbiosis between a marine alga and a N-2-fixing cyanobacterium (Cyanobacterium UCYN-A) is geographically widespread in the oceans and is important in the marine N cycle. UCYN-A is uncultivated and is an unusual unicellular cyanobacterium because it lacks many metabolic functions, including oxygenic photosynthesis and carbon fixation, which are typical in cyanobacteria. It is now presumed to be an obligate symbiont of haptophytes closely related to Braarudosphaera bigelowii. N-2-fixing cyanobacteria use different strategies to avoid inhibition of N-2 fixation by the oxygen evolved in photosynthesis. Most unicellular cyanobacteria temporally separate the two incompatible activities by fixing N-2 only at night, but, surprisingly, UCYN-A appears to fix N-2 during the day. The goal of this study was to determine how the unicellular UCYN-A strain coordinates N-2 fixation and general metabolism compared to other marine cyanobacteria. We found that UCYN-A has distinct daily cycles of many genes despite the fact that it lacks two of the three circadian clock genes found in most cyanobacteria. We also found that the transcription patterns in UCYN-A are more similar to those in marine cyanobacteria that are capable of aerobic N-2 fixation in the light, such as Trichodesmium and heterocyst-forming cyanobacteria, than to those in Crocosphaera or Cyanothece species, which are more closely related to unicellular marine cyanobacteria evolutionarily. Our findings suggest that the symbiotic interaction has resulted in a shift of transcriptional regulation to coordinate UCYN-A metabolism with that of the phototrophic eukaryotic host, thus allowing efficient coupling of N-2 fixation (by the cyanobacterium) to the energy obtained from photosynthesis (by the eukaryotic unicellular alga) in the light. IMPORTANCE The symbiotic N-2-fixing cyanobacterium UCYN-A, which is closely related to Braarudosphaera bigelowii, and its eukaryotic algal host have been shown to be globally distributed and important in open-ocean N-2 fixation. These unique cyanobacteria have reduced metabolic capabilities, even lacking genes for oxygenic photosynthesis and carbon fixation. Cyanobacteria generally use energy from photosynthesis for nitrogen fixation but require mechanisms for avoiding inactivation of the oxygen-sensitive nitrogenase enzyme by ambient oxygen (O-2) or the O-2 evolved through photosynthesis. This study showed that symbiosis between the N-2-fixing cyanobacterium UCYN-A and its eukaryotic algal host has led to adaptation of its daily gene expression pattern in order to enable daytime aerobic N-2 fixation, which is likely more energetically efficient than fixing N-2 at night, as found in other unicellular marine cyanobacteria.

  • 88.
    del Valle, Daniela A.
    et al.
    University of Hawaii, USA.
    Martínez-García, Sandra
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Hawaii, USA.
    Sañudo-Wilhelmy, Sergio A.
    University of Southern California, USA.
    Kiene, Ronald P.
    University of South Alabama, USA ; Dauphin Island Sea Lab, USA.
    Karl, David M.
    University of Hawaii, USA.
    Methionine and dimethylsulfoniopropionate as sources of sulfur to the microbial community of the North Pacific Subtropical Gyre2015In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 75, no 2, p. 103-116Article in journal (Refereed)
    Abstract [en]

    Methionine (Met) and dimethylsulfoniopropionate (DMSP) are 2 important substrates that can serve as sources of sulfur and carbon to microbial communities in the sea. We studied the vertical and diel distributions and the assimilation rates of dissolved Met (dMet) and dissolved DMSP (dDMSP) into proteins of different microbial groups at Stn ALOHA, in the oligotrophic North Pacific Subtropical Gyre (NPSG). Concentrations of dMet never exceeded 50 pM and were at their daily minimum during the night-time (<0.17 pM). dMet assimilation into proteins accounted for <30% of the dMet lost from the dissolved pool, suggesting that other metabolic pathways were also important. Concentrations of dDMSP ranged from 0.35 to 1.0 nM in surface waters and did not present a distinguishable diel pattern. Cell-sorted Prochlorococcus, high nucleic acid (HNA), and low nucleic acid (LNA) non-pigmented bacteria showed a clear diel pattern for dMet and dDMSP assimilation, with higher rates during the night-time. Among the different groups, HNA bacteria had the highest per-cell assimilation rate for dMet and dDMSP, but when accounting for cell numbers in each group, the HNA and LNA bacterial group assimilation rates were comparable for both dDMSP and dMet. Integrated water column (0 to 125 m) dDMSP assimilation rates by the entire microbial assemblage were 1.7- To 5.3-fold faster than those for dMet, suggesting that dDMSP constitutes a more important source of sulfur than dMet to the microbial community of the NPSG during the time of our study.

  • 89.
    Dinasquet, Julie
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Substrate control of community composition and functional adaptation in marine bacterioplankton2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A drop of sea-water is teeming with a million of bacteria, on which pelagic food-webs and biogeochemical cycles depend. These bacteria thrive on a wide range of dissolved organic carbon (DOC) compounds produced through biotic and abiotic processes. Molecular analyses have over the past decades shown that specific bacterial taxa differ in their capacity to exploit DOC, suggesting a tight link between bacterial community composition (BCC) and ocean biogeo-chemistry. Therefore, an understanding of how resource availability and mortality agents drive BCC and bacterial functional adaptation is a prerequisit for predictions of how marine ecosystems will respond to future global change.

    In this thesis, I have studied BCC and bacterial functionality in response to various controlling factors relevant in an environmental changes perspective. For instance, the extensive regional warming in Antarctica induces the proliferation of icebergs. By investigating the bacterioplankton in the surrounding of a drifting iceberg, hydrographical perturbations driven by the iceberg were found to affect BCC, functionality and the capacity of indigenous taxa to utilize specific DOC compounds. Furthermore, a study of community succession during DOC utilization assays demonstrated that bacterial assemblages adapt to the gradual exhaustion of available DOC through community compositional succession. In addition, the variation in substrate availability and temperature may also affect BCC in eutrophic systems.

    While substrate availability can have an important impact on BCC and bacterial functionality, it is also important to study the cascading effects of higher trophic levels on bacteria. During a mesocosm experiment, the presence of an invasive gelatinous top-predator was shown to have only limited effects on the structure and function of the bacterial community in the Baltic Sea due to nutrient limiting conditions and to the overall complexity of the food-web. However, this top-predator may have direct bottom-up impact on bacteria in its close surrounding.

    The results presented in this thesis show that the bacterioplankton is sensitive to the availability of substrates and that bacterial community composition responds to contemporary environmental conditions. These results contribute to our understanding of how ecosystem disturbances affect marine bacterioplankton; insights of relevance to biogeochemistry and food-webs in the oceans.

  • 90.
    Dinasquet, Julie
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. University of Copenhagen, Denmark.
    Granhag, Lena
    University of Gothenburg ; Chalmers University of Technology.
    Riemann, Lasse
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Stimulated bacterioplankton growth and selection for certain bacterial taxa in the vicinity of the ctenophore Mnemiopsis leidyi2012In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 3, article id 302Article in journal (Refereed)
    Abstract [en]

    Episodic blooms of voracious gelatinous zooplankton, such as the ctenophore Mnemiopsis leidyi, affect pools of inorganic nutrients and dissolved organic carbon by intensive grazing activities and mucus release. This will potentially influence bacterioplankton activity and community composition, at least at local scales; however, available studies on this are scarce. In the present study we examined effects of M. leidyi on bacterioplankton growth and composition in incubation experiments. Moreover, we examined community composition of bacteria associated with the surface and gut of M. leidyi. High release of ammonium and high bacterial growth was observed in the treatments with M. leidyi relative to controls. Deep 454 pyrosequencing of 16 S rRNA genes showed specific bacterial communities in treatments with M. leidyi as well as specific communities associated with M. leidyi tissue and gut. In particular, members of Flavobacteriaceae were associated with M. leidyi. Our study shows that M. leidyi influences bacterioplankton activity and community composition in the vicinity of the jellyfish. In particular during temporary aggregations of jellyfish, these local zones of high bacterial growth may contribute significantly to the spatial heterogeneity of bacterioplankton activity and community composition in the sea.

  • 91.
    Dinasquet, Julie
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Copenhagen, Denmark ; Scripps Inst Oceanography, USA.
    Richert, Inga
    Uppsala University ; UFZ Helmholtz Ctr Environm Res, Germany.
    Logares, Ramiro
    CSIC, Spain.
    Yager, Patricia
    Univ Georgia, USA.
    Bertilsson, Stefan
    Uppsala University.
    Riemann, Lasse
    Univ Copenhagen, Denmark.
    Mixing of water masses caused by a drifting iceberg affects bacterial activity, community composition and substrate utilization capability in the Southern Ocean2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 6, p. 2453-2467Article in journal (Refereed)
    Abstract [en]

    The number of icebergs produced from ice-shelf disintegration has increased over the past decade in Antarctica. These drifting icebergs mix the water column, influence stratification and nutrient condition, and can affect local productivity and food web composition. Data on whether icebergs affect bacterioplankton function and composition are scarce, however. We assessed the influence of iceberg drift on bacterial community composition and on their ability to exploit carbon substrates during summer in the coastal Southern Ocean. An elevated bacterial production and a different community composition were observed in iceberg-influenced waters relative to the undisturbed water column nearby. These major differences were confirmed in short-term incubations with bromodeoxyuridine followed by CARD-FISH. Furthermore, one-week bottle incubations amended with inorganic nutrients and carbon substrates (a mix of substrates, glutamine, Nacetylglucosamine, or pyruvate) revealed contrasting capacity of bacterioplankton to utilize specific carbon substrates in the iceberg-influenced waters compared with the undisturbed site. Our study demonstrates that the hydrographical perturbations introduced by a drifting iceberg can affect activity, composition, and substrate utilization capability of marine bacterioplankton. Consequently, in a context of global warming, increased frequency of drifting icebergs in polar regions holds the potential to affect carbon and nutrient biogeochemistry at local and possibly regional scales.

  • 92.
    Doane, Marie
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sarenbo, Sirkku
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    An eradication attempt of Mycoplasma spp. mastitis at a large dairy farm in NY State, USA2015In: IOCH 2015, 2015Conference paper (Refereed)
  • 93.
    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)
  • 94.
    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.

  • 95.
    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.

  • 96.
    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.

  • 97.
    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.

  • 98.
    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.

  • 99.
    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.

  • 100.
    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.

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