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  • 1.
    Abdelfattah, Ahmed
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Germany; Graz University of Technology, Austria .
    Tack, Ayco J. M.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Lobato, Carolina
    Wassermann, Birgit
    Berg, Gabriele
    From seed to seed: the role of microbial inheritance in the assembly of the plant microbiome2023In: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 31, no 4, p. 346-355Article, review/survey (Refereed)
    Abstract [en]

    Despite evidence that the microbiome extends host genetic and phenotypic traits, information on how the microbiome is transmitted and maintained across generations remains fragmented. For seed-bearing plants, seeds harbor a distinct microbiome and play a unique role by linking one generation to the next. Studies on microbial inheritance, a process we suggest including both vertical transmission and the subsequent migration of seed microorganisms to the new plant, thus become essential for our understanding of host evolutionary potential and host–microbiome coevolution. We propose dividing the inheritance process into three stages: (i) plant to seed, (ii) seed dormancy, and (iii) seed to seedling. We discuss the factors affecting the assembly of the microbiome during the three stages, highlight future research directions, and emphasize the implications of microbial inheritance for fundamental science and society.

  • 2.
    Ahmed, Engy
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holmström, Sara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Soil Microorganisms and Mineral Weathering: Mechanics of Biotite Dissolution2012Conference paper (Other academic)
    Abstract [en]

    Soil microorganisms play an important role in the environment by contributing to leach and release of essential elements from soil minerals that are required not only for their own nutrition but also for plants growth. This study aims to compare between the mechanisms of different fungal and bacterial species isolated from podzol soil in biotite dissolution. Microplate devices with 6 wells were used for the biological weathering experiments. All of the sterilized microplate wells were filled with 4g/l of biotite followed by 12 ml of an iron free diluted mineral liquid medium. In these conditions, biotite particles are the only source of the essential elements for the microorganisms. To characterize the mechanisms of biotite dissolution, we monitored siderophores production, microbial biomass, pH, exchangeable cations concentration and SEM analysis for mineral surface. There was a significant difference between the behavior of the fungal and bacterial species in dissolution of biotite. This difference may be due to the variation of these microorganisms in their mechanics of interaction with mineral surface. It was observed also that these microorganisms directly and indirectly induce biotite dissolution. Defining soil as a system driven by biological mechanisms rather than chemical processes has major implications for our understanding of how the system functions and how it will respond to changing conditions.

  • 3.
    Ahmed, Engy
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holmström, Sara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    THE MICROBE-MINERAL INTERACTIONS IN THE ACIDIC PODZOL SOIL2013In: Mineralogical magazine, ISSN 0026-461X, E-ISSN 1471-8022, Vol. 77, no 5, p. 564-Article in journal (Other (popular science, discussion, etc.))
    Abstract [en]

    Iron is a key component of the chemical architecture of the biosphere. Due to the low bioavailability of iron in the environment, microorganisms have developed specific uptake strategies, like siderophores, which are operationally defined as low-molecular-mass biogenic Fe(III)-binding compounds, that can increase iron’s bioavailability by promoting the dissolution of iron-bearing minerals. In the present study, we aimed to investigate the composition of hydroxamate siderophores in the soil horizons of the acidic podzol, and study how they are affected by the presence of specific mineral types and microbial communities.

     Three different minerals (apatite, biotite and oligioclase) were inserted in the soil horizons (O (organic), E (eluvial), B (upper illuvial), and C (mineral)). After two years, soil samples were collected from both the bulk soil (next to the minerals) and from the soil attached to the mineral surfaces. The concentration of ten different fungal tri-hydroxamates and five bacterial ones were determined by high-performance liquid chromatography coupled to electrospray ionization mass spectrometry (HPLC-ESI-MS). In addition, total microbial composition and diversity were studied.

    Our field experiment succeeded in describing the relationship between the presence of siderophores, soil horizon and mineral type, in addition to understanding the interaction between mineral type and soil microbial composition. A wide range of fungal and bacterial hydroxamates were detected throughout the soil profile. On the other hand, the presence of the minerals completely altered the diversity of siderophores. In addition, each mineral had a unique interaction with hydroxamates in the different soil horizons. There were also a good relationship between the microbial diversity and the siderophore distribution. 

  • 4.
    Ahmed, Engy
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holmström, Sara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    The Roles and Applications of Siderophores in Natural Environments2013Conference paper (Other academic)
    Abstract [en]

    Siderophores are organic compounds with low molecular mass that are produced by microorganisms growing under conditions of low iron. The primary function of these compounds is to chelate ferric iron from different terrestrial and aquatic habitats and thereby make it available for microbial cells.

    Siderophores have received much attention in recent years because of their potential roles and applications in various areas of environmental research. For instance, the production of siderophores can provide a quick identification of microbes to the species level that called “siderotyping”. On the other hand, siderophores could also function as biocontrol, biosensor, and bioremediation agents, in addition to their important role in mineral weathering and enhancing plant growth. In the present study, we aimed to investigate the composition of trihydroxamate siderophores in soil samples from different horizons (O (organic), E (eluvial), B (upper illuvial), and C (parent material)) of a podzol soil in Sweden, and study how they are affected by the presence of specific mineral types (apatite, biotite and oligioclase) that were inserted in the soil for two years in a field experiment.

    Our field experiment succeeded in describing the relationship between the presence of siderophores, soil horizons and mineral types. A wide range of fungal and bacterial hydroxamates were detected throughout the soil profile. On the other hand, the presence of the minerals completely altered the diversity of siderophores. In addition, each mineral had a unique interaction with hydroxamates in the different soil horizons. Our next step is to gain greater insight into the siderotyping to illustrate the relationship between the siderophore types that was found throughout the soil profile and on the different mineral surfaces and the microbial diversity by using metagenomic applications.

  • 5.
    Ahmed, Engy
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holmström, Sara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Brüchert, Volker
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holm, Nils G.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    The Role of Microorganisms in the diversity and distribution of siderophores in Podzolic Forest Soil2013In: Mineralogical magazine, ISSN 0026-461X, E-ISSN 1471-8022, Vol. 77, no 2, p. 161--208(48)Article in journal (Other academic)
    Abstract [en]

    Iron is a key component of the chemical architecture of the biosphere. Due to the low bioavailability of iron in the environment, microorganisms have developed specific uptake strategies. The most important one is the production of siderophores, which are operationally defined as low-molecular-mass biogenic Fe (III)-binding compounds which may greatly increase bioavailability of Fe [1]. One of the primary biogeochemical functions of siderophores is therefore to increase Fe bioavailability by promoting the dissolution of iron-bearing minerals [2]. This study aims to understand the role of microorganisms in the chemical diversity and distribution of siderophores in podzol soil and how this diversity can contribute to the bioavailability of Fe in forest soil.Soil samples were collected from an experimental site in the area of Bispgården in central Sweden (63°07′N, 16°70′E) from the O (organic), E (eluvial), B1 (upper illuvial), and C (mineral) horizons. Concentration and chemical composition of dissolved and adsorbed siderophores in the soil samples were determined using colorimetric assays and high-performance liquid chromatography.The highest siderophore concentrations were found in the O layer and thereafter decreased by depth. Concentrations of dissolved hydroxamate, catecholate and carboxylate siderophores were up to 84, 17 and 0.2 nmol/ g soil, respectively. In contrast, concentrations of adsorbed hydroxamates, catecholates and carboxylates were only up to 1.8, 3 and 0.2 nmol/ g soil, respectively.Siderophore-producing microorganisms were isolated from the same soil samples. Viable fungi, bacteria and actinomycete counts ranged from 7 to 300, from 300 to 1800, and from 0 to 5 cfu/gm, respectively. The highest counts were found in the O and E layers. Only the E layer contained the three types of siderophore-producing microorganisms investigated in this study. Siderophores were extracted from culture filtrates of the isolated microorganisms when grown under iron-limited conditions. These extracts varied considerably in siderophore composition. Fungal isolates produced up to 183 μM of hydroxamates, especially those isolated from the O layer, whereas bacteria and actinomycete isolated from the O and E layers of the soil produced high amounts of carboxylate, catecholate and hydroxamate siderophores. Actinomycete produced up to 93 μM of hydroxamates and 47 μM of catecholates, while bacteria produced up to 34 μM of carboxylates and up to 14 μM of catecholates.The depth variability in concentration and chemical composition and the good correlation between abundance of siderophore-producing microorganisms and siderophore soil concentrations strongly suggest that these siderophore-producing microorganisms play an important role in the mobilization of iron in the podzol soil that may be important in iron availability to plants in forest environment.

    [1] Clay et al. (1981) Biochemistry 20, 2432-2436. [2] Duckworth et al. (2009) ChemGeol 260, 149-158.

  • 6.
    Akar, Roya
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Fink, Matthias J.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Omnus, Deike J.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Jonas, Kristina
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Regulation of the general stress response sigma factor σT by Lon-mediated proteolysis2023In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 205, no 11Article in journal (Refereed)
    Abstract [en]

    The Lon protease is widely conserved in both prokaryotic and eukaryotic organisms and fulfills important regulatory functions. Nevertheless, the number of identified Lon substrates is limited in most organisms, and the precise role of Lon in regulating these proteins is poorly understood. Here, we describe the α-proteobacterial general stress response sigma factor σT as a novel Lon substrate in Caulobacter crescentus. Based on previously published quantitative proteomics data, we find σT to be a promising putative Lon substrate and confirm a direct role of Lon in degrading σT. We show that Lon contributes to the downregulation of σT abundance under optimal conditions and during recovery from sucrose-induced osmotic stress. Furthermore, the presence of the Lon activity regulator LarA enhances Lon-mediated degradation of σT in vitro and reduces σT levels in vivo indicating a role of LarA in modulating Lon-mediated degradation of σT. Together, our results highlight the importance of Lon during the recovery phase following stress exposure by adjusting the concentrations of critical regulators of stress responses.

  • 7.
    Albert, Séréna
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Benthic-pelagic coupling in a changing world: Structural and functional responses of microbenthic communities to organic matter settling2021Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Marine soft sediments form the second largest habitat on the planet. Organisms residing in this environment represent a vast reservoir of biodiversity, and play key roles in ecosystem processes. Most benthic organisms depend on organic matter (OM) inputs from phytoplankton in the overlying water column as food supply, but human impacts such as eutrophication and climate change are profoundly altering natural ecosystem dynamics. The consequences of changes in benthic-pelagic coupling for the biodiversity and functioning of soft-sediment communities have yet to be resolved. 

    The aim of this thesis is to assess the role of OM settling on soft-sediments microeukaryotic (small organisms < 1 mm) and bacterial communities. The intents are two-fold, to investigate impacts on (1) community structure and diversity (chapters I, II and IV); and (2) ecosystem functioning, notably in relation to nitrogen (N) cycling (chapters I and III). 

    Our results show that settling OM quantity and quality both had a significant impact on microeukaryotic alpha-diversity. We observed a decrease in alpha-diversity following settling of diatom-derived spring bloom OM, possibly as a result of competitive exclusion, while cyanobacteria-derived summer bloom OM did not affect alpha-diversity (chapters I and IV). We also found that high biomass of diatoms and others fast sinking phytoplankton groups in the water column led to lower microeukaryotic alpha diversity after this material settled on the seafloor (chapter IV). Presumably, following this large sedimentation event, sediment oxygen (O2) demand was strongly stimulated, excluding O2-sensitive taxa. Overall, we propose that the assembly of microeukaryotic communities was primarily mediated by OM settling quantity (chapter IV), while differences in OM quality led to significant but more subtle changes, occurring at fine taxonomic level (chapter I). The response of bacterial communities to OM settling was less pronounced, and probably restricted to the uppermost sediment layer (chapters I and IV). We did, however, observe a significant effect of OM quality on bacterial communities assembly at the sediment-water interface, with taxa favored either by diatom- or by cyanobacteria-derived OM (chapter II). This study also showed that feedback mechanisms from nutrient recycling in the sediment could play a role in this response. Finally, our results indicated a substantial influence of OM quality on N cycling at the sediment-water interface. We found that settling of fresh OM (i.e. low C:N ratio) stimulated denitrification activity (chapters I and III), while simultaneously promoting more N recycling to the water column than settling of degraded OM (i.e. high C:N ratio) did (chapter III).  

    Altogether, our results indicate that current changes in OM settling dynamics in marine systems will likely impact microeukaryotic and, to some extent, bacterial biodiversity in soft sediments. Alterations in settling OM quality, in particular, may also affect crucial microbial processes involved in N cycling. This thesis highlights the importance of considering benthic-pelagic coupling mechanisms to better understand likely future changes in marine ecosystems.

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  • 8.
    Andersson, Kerstin
    Stockholm University.
    Anti-microbial defense molecules from the cecropia moth1989Doctoral thesis, comprehensive summary (Other academic)
  • 9.
    Ankarklev, Johan
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Lebbad, Marianne
    Einarsson, Elin
    Franzen, Oscar
    Ahola, Harri
    Troell, Karin
    Svard, Staffan G.
    A novel high-resolution multilocus sequence typing of Giardia intestinalis Assemblage A isolates reveals zoonotic transmission, clonal outbreaks and recombination2018In: Infection, Genetics and Evolution, ISSN 1567-1348, E-ISSN 1567-7257, Vol. 60, p. 7-16Article in journal (Refereed)
    Abstract [en]

    Molecular epidemiology and genotyping studies of the parasitic protozoan Giardia intestinalis have proven difficult due to multiple factors, such as low discriminatory power in the commonly used genotyping loci, which has hampered molecular analyses of outbreak sources, zoonotic transmission and virulence types. Here we have focused on assemblage A Giardia and developed a high-resolution assemblage-specific multilocus sequence typing (MLST) method. Analyses of sequenced G. intestinalis assemblage A genomes from different sub-assemblages identified a set of six genetic loci with high genetic variability. DNA samples from both humans (n = 44) and animals (n = 18) that harbored Giardia assemblage A infections, were PCR amplified (557-700 bp products) and sequenced at the six novel genetic loci. Bioinformatic analyses showed five to ten-fold higher levels of polymorphic sites than what was previously found among assemblage A samples using the classic genotyping loci. Phylogenetically, a division of two major clusters in assemblage A became apparent, separating samples of human and animal origin. A subset of human samples (n = 9) from a documented Giardia outbreak in a Swedish day-care center, showed full complementarity at nine genetic loci (the six new and the standard BG, TPI and GDH loci), strongly suggesting one source of infection. Furthermore, three samples of human origin displayed MLST profiles that were phylogenetically more closely related to MLST profiles from animal derived samples, suggesting zoonotic transmission. These new genotyping loci enabled us to detect events of recombination between different assemblage A isolates but also between assemblage A and E isolates. In summary, we present a novel and expanded MLST strategy with significantly improved sensitivity for molecular analyses of virulence types, zoonotic potential and source tracking for assemblage A Giardia.

  • 10. Arroyo, Nina Larissa
    et al.
    Aarnio, Katri
    Olafsson, Emil
    Stockholm University, Faculty of Science, Department of Zoology.
    Interactions between two closely related phytal harpacticoid copepods, asymmetric positive and negative effects2007In: Journal of Experimental Marine Biology and Ecology, ISSN 0022-0981, E-ISSN 1879-1697, Vol. 341, no 2, p. 219-227Article in journal (Refereed)
    Abstract [en]

    Competition for food is generally thought to exert a strong evolutionary pressure, driving trophic niche separation, either by specialization and/or by widening the choice of potential food resources. Harpacticoid copepods are common inhabitants of phytal assemblages, where several closely related species of the so-called phytal dwelling families often co-occur. However, direct competition among phytal harpacticoids has been thought to be unlikely, due to the abundant and continuously available food supplies. We conducted a series of field and laboratory studies to assess the role of competition in the abundance distribution of two closely related harpacticoid species, Mesochra rapiens and M. aestuari. We found that the abundance of both species co-varied on several seaweed species in the northern Baltic Sea, during a 3-month period. Stable isotope ratios in the green alga Cladophora glomerata field samples indicated different resource utilization of the two species, both in fresh and deteriorated C. glomerata, and in drifting algae. We tested in the laboratory if resource utilization was different between the species in sympatry and allopatry. We used enriched stable carbon isotope ratios (C-13/C-12) of the diatom Phaeodactylum tricornutum to trace the uptake in both species. Results from these experiments showed a much higher assimilation by M. aestuari in sympatry with M. rapiens, while the latter species showed a higher assimilation in allopatry. Our results show that while there is no apparent competition for resources between these two species in the field, there seems to be an asymmetric reaction when in sympatry and provided one single resource in the laboratory. We suggest that M. rapiens may facilitate assimilation by M. acstuari and discuss the mechanisms by which this may take place.

  • 11.
    Balk, Lennart
    et al.
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Hägerroth, Per-Ake
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Åkerman, Gun
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Hanson, Marsha
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Tjärnlund, Ulla
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Hansson, Tomas
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Hallgrimsson, Gunnar Thor
    Zebühr, Yngve
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Broman, Dag
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Mörner, Torsten
    Sundberg, Henrik
    Wild birds of declining European species are dying from a thiamine deficiency syndrome.2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 29, p. 12001-12006Article in journal (Refereed)
    Abstract [en]

    Wild birds of several species are dying in large numbers from an idiopathic paralytic disease in the Baltic Sea area. Here, we demonstrate strong relationships between this disease, breeding failure, and thiamine (vitamin B(1)) deficiency in eggs, pulli, and full-grown individuals. Thiamine is essential for vertebrates, and its diphosphorylated form functions as a cofactor for several life sustaining enzymes, whereas the triphosphorylated form is necessary for the functioning of neuronal membranes. Paralyzed individuals were remedied by thiamine treatment. Moreover, thiamine deficiency and detrimental effects on thiamine-dependent enzymes were demonstrated in the yolk, liver, and brain. We propose that the mortality and breeding failure are part of a thiamine deficiency syndrome, which may have contributed significantly to declines in many bird populations during the last decades.

  • 12.
    Baltscheffsky, Margareta
    Stockholm University.
    Inorganic pyrophosphate and reversed energy conversion reactions in bacterial photophosphorylation: a study with the chromatophore system of the photosynthetic bacterium rhodospirillum rubrum1969Doctoral thesis, comprehensive summary (Other academic)
  • 13. Barisic, Ivan
    et al.
    Schoenthaler, Silvia
    Ke, Rongqin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Nilsson, Mats
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Noehammer, Christa
    Wiesinger-Mayr, Herbert
    Multiplex detection of antibiotic resistance genes using padlock probes2013In: Diagnostic microbiology and infectious disease, ISSN 0732-8893, E-ISSN 1879-0070, Vol. 77, no 2, p. 118-125Article in journal (Refereed)
    Abstract [en]

    The elucidation of resistance mechanisms is of central importance to providing and maintaining efficient medical treatment. However, molecular detection methods covering the complete set of resistance genes with a single test are still missing. Here, we present a novel 100-plex assay based on padlock probes in combination with a microarray that allows the simultaneous large-scale identification of highly diverse beta-lactamases. The specificity of the assay was performed using 70 clinical bacterial isolates, recovering 98% of the beta-lactamase nucleotide sequences present. Additionally, the sensitivity was evaluated with PCR products and genomic bacterial DNA, revealing a detection limit of 10(4) DNA copies per reaction when using PCR products as the template. Pre-amplification of genomic DNA in a 25-multiplex PCR further facilitated the detection of beta-lactamase genes in dilutions of 10(7) cells/mL. In summary, we present an efficient, highly specific, and highly sensitive multiplex detection method for any gene.

  • 14.
    Basmarke-Wehelie, Rahma
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Sjölinder, Hong
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Jurkowski, Wiktor
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Elofsson, Arne
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Arnqvist, Anna
    Umea Univ, Dept Med Biochem & Biophys, Sweden.
    Engstrand, Lars
    Karolinska Inst, Swedish Inst Infect Dis Control, Sweden.
    Hagner, Matthias
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Wallin, Elin
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Guan, Na
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Kuranasekera, Hasanthi
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Aro, Helena
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Jonsson, Ann-Beth
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    The complement regulator CD46 is bactericidal to Helicobacter pylori and blocks urease activity2011In: Gastroenterology, ISSN 0016-5085, E-ISSN 1528-0012, Vol. 141, no 3, p. 918-928Article in journal (Refereed)
    Abstract [en]

    BACKGROUND & AIMS: CD46 is a C3b/C4b binding complement regulator and a receptor for several human pathogens. We examined the interaction between CD46 and Helicobacter pylori (a bacterium that colonizes the human gastric mucosa and causes gastritis), peptic ulcers, and cancer.

    METHODS: Using gastric epithelial cells, we analyzed a set of H pylori strains and mutants for their ability to interact with CD46 and/or influence CD46 expression. Bacterial interaction with full-length CD46 and small CD46 peptides was evaluated by flow cytometry, fluorescence microscopy, enzyme-linked immunosorbent assay, and bacterial survival analyses.

    RESULTS: H pylori infection caused shedding of CD46 into the extracellular environment. A soluble form of CD46 bound to H pylori and inhibited growth, in a dose- and time-dependent manner, by interacting with urease and alkyl hydroperoxide reductase, which are essential bacterial pathogenicity-associated factors. Binding of CD46 or CD46-derived synthetic peptides blocked the urease activity and ability of bacteria to survive in acidic environments. Oral administration of one CD46 peptide eradicated H pylori from infected mice.

    CONCLUSIONS: CD46 is an antimicrobial agent that can eradicate H pylori. CD46 peptides might be developed to treat H pylori infection.

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  • 15.
    Baumgarten, Thomas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Protein production in the E. coli cell envelope2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Proteins fulfil essential functions in every cell and malfunctioning proteins are often the cause of diseases. On the other hand, proteins like antibody fragments or hormones can be used to treat diseases. Proteins are often produced in the bacterium Escherichia coli so that they can be studied to understand their (mal)function or so that they can be used to treat a disease. Unfortunately, producing proteins in the cell envelope of E. coli, like integral membrane proteins, which are important drug targets, and secretory proteins like antibody fragments and hormones, often results in unsatisfactory yields. Therefore, the objectives of this doctoral thesis were to identify bottlenecks that can limit the production of recombinant proteins in the cell envelope of E. coli and to try to overcome these bottlenecks. In the first study, we isolated and characterized the E. coli membrane protein production strain Mt56(DE3). This strain, in which the target gene expression intensity is strongly reduced, outcompetes the standard E. coli membrane protein production strains for most targets tested. In the second and third study we focused on the production of secretory proteins, i.e., proteins that are translocated across the inner membrane into the periplasm of E. coli. First, we investigated the impact of the targeting pathway used to direct a secretory protein to the translocation machinery on the cell physiology and protein production yields. We found that the co-translational targeting of a produced protein saturates the capacity of the translocation machinery resulting in heavily impaired biomass formation and low protein production yields. In contrast, post-translational targeting of a produced protein did not saturate the capacity of the protein translocation machinery resulting in hardly affected biomass formation and high protein production yields. In the third study we investigated how optimizing the production of a co-translationally targeted protein, by harmonizing its production rate with the capacity of the protein translocation machinery, affects the physiology of the cell. We found that, in stark contrast to the non-optimized condition, the optimized production did not affect the composition of the E. coli proteome. This surprising finding indicates that a protein can be produced efficiently in the periplasm of E. coli without compromising the physiology of the cell. In the last study we aimed at developing an outer membrane vesicle-based tuberculosis vaccine. To this end, an E. coli strain was created that produced outer membrane vesicles coated with different tuberculosis antigens. It was shown that a homogenous population of vesicles was produced, which will hopefully facilitate the isolation of these vesicles on an industrial scale.

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  • 16. Bengtsson-Palme, Johan
    et al.
    Angelin, Martin
    Huss, Mikael
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Kjellqvist, Sanela
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Kristiansson, Erik
    Palmgren, Helena
    Larsson, D. G. Joakim
    Johansson, Anders
    The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents2015In: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 59, no 10, p. 6551-6560Article in journal (Refereed)
    Abstract [en]

    Previous studies of antibiotic resistance dissemination by travel have, by targeting only a select number of cultivable bacterial species, omitted most of the human microbiome. Here, we used explorative shotgun metagenomic sequencing to address the abundance of >300 antibiotic resistance genes in fecal specimens from 35 Swedish students taken before and after exchange programs on the Indian peninsula or in Central Africa. All specimens were additionally cultured for extended-spectrum beta-lactamase (ESBL)-producing enterobacteria, and the isolates obtained were genome sequenced. The overall taxonomic diversity and composition of the gut microbiome remained stable before and after travel, but there was an increasing abundance of Proteobacteria in 25/35 students. The relative abundance of antibiotic resistance genes increased, most prominently for genes encoding resistance to sulfonamide (2.6-fold increase), trimethoprim (7.7-fold), and beta-lactams (2.6-fold). Importantly, the increase observed occurred without any antibiotic intake. Of 18 students visiting the Indian peninsula, 12 acquired ESBL-producing Escherichia coli, while none returning from Africa were positive. Despite deep sequencing efforts, the sensitivity of metagenomics was not sufficient to detect acquisition of the low-abundant genes responsible for the observed ESBL phenotype. In conclusion, metagenomic sequencing of the intestinal microbiome of Swedish students returning from exchange programs in Central Africa or the Indian peninsula showed increased abundance of genes encoding resistance to widely used antibiotics.

  • 17.
    Berckx, Fede
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Bandong, Cyndi Mae
    Wibberg, Daniel
    Kalinowski, Jörn
    Simbahan, Jessica
    Pawlowski, Katharina
    Streptomyces benguetensis sp. nov., a novel streptomycete isolated from actinorhizal nodules of Coriaria intermediaManuscript (preprint) (Other academic)
  • 18.
    Berger, Urs
    et al.
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Glynn, Anders
    Holmström, Katrin E
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Berglund, Marika
    Ankarberg, Emma Halldin
    Törnkvist, Anna
    Fish consumption as a source of human exposure to perfluorinated alkyl substances in Sweden: analysis of edible fish from Lake Vättern and the Baltic Sea2009In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 76, no 6, p. 799-804Article in journal (Refereed)
    Abstract [en]

    Perfluorinated alkyl substances (PFAS) were analyzed in muscle tissue from edible fish species caught in the second largest freshwater lake in Sweden, Lake Vättern (LV), and in the brackish water Baltic Sea (BS). Perfluorooctane sulfonate (PFOS) was the predominant PFAS found. PFOS concentrations were higher in LV (medians 2.9-12 ng g(-1) fresh weight) than in BS fish (medians 1.0-2.5 ng g(-1) fresh weight). Moreover, LV fish was more contaminated with several other PFAS than BS fish. This may be due to anthropogenic discharges from urban areas around LV. The PFAS pattern differed between LV and BS fish, indicating different sources of contamination for the two study areas. Human exposure to PFOS via fish intake was calculated for three study groups, based on consumption data from literature. The groups consisted of individuals that reported moderate or high consumption of BS fish or high consumption of LV fish, respectively. The results showed that PFOS intake strongly depended on individual fish consumption as well as the fish catchment area. Median PFOS intakes were estimated to 0.15 and 0.62 ng kg(-1) body weight (bw) d(-1) for the consumers of moderate and high amounts of BS fish, respectively. For the group with high consumption of LV fish a median PFOS intake of 2.7 ng kg(-1)bw d(-1) was calculated. Fish consumption varied considerably within the consumer groups, with maximum PFOS intakes of 4.5 (BS fish) or 9.6 ng kg(-1)bw d(-1) (LV fish). Comparison of our results with literature data on PFOS intake from food suggests that fish from contaminated areas may be a significant source of dietary PFOS exposure.

  • 19.
    Bergman, Birgitta
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Sandh, Gustaf
    Stockholm University, Faculty of Science, Department of Botany.
    Lin, Senjie
    Larsson, John
    Stockholm University, Faculty of Science, Department of Botany.
    Carpenter, Edward J.
    Trichodesmium - a widespread marine cyanobacterium with unusual nitrogen fixation properties2013In: FEMS Microbiology Reviews, ISSN 0168-6445, E-ISSN 1574-6976, Vol. 37, no 3, p. 286-302Article, review/survey (Refereed)
    Abstract [en]

    The last several decades have witnessed dramatic advances in unfolding the diversity and commonality of oceanic diazotrophs and their N2-fixing potential. More recently, substantial progress in diazotrophic cell biology has provided a wealth of information on processes and mechanisms involved. The substantial contribution by the diazotrophic cyanobacterial genus Trichodesmium to the nitrogen influx of the global marine ecosystem is by now undisputable and of paramount ecological importance, while the underlying cellular and molecular regulatory physiology has only recently started to unfold. Here, we explore and summarize current knowledge, related to the optimization of its diazotrophic capacity, from genomics to ecophysiological processes, via, for example, cellular differentiation (diazocytes) and temporal regulations, and suggest cellular research avenues that now ought to be explored.

  • 20.
    Björnsson, Ásgeir
    Stockholm University, Faculty of Science.
    The influence of codon context on translation termination and messenger RNA levels1994Doctoral thesis, comprehensive summary (Other academic)
  • 21.
    Broman, Elias
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre. Södertörn University, Sweden.
    Abdelgadir, Mohanad
    Bonaglia, Stefano
    Forsberg, Sara
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Södertörn University, Sweden.
    Wikström, Johan
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Gunnarsson, Jonas S.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Nascimento, Francisco J. A.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre.
    Sjöling, Sara
    Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities2023In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 86, no 4, p. 2357-2372Article in journal (Refereed)
    Abstract [en]

    Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.

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  • 22.
    Broman, Elias
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre.
    Zilius, Mindaugas
    Samuiloviene, Aurelija
    Vybernaite-Lubiene, Irma
    Politi, Tobia
    Klawonn, Isabell
    Voss, Maren
    Nascimento, Francisco J. A
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre.
    Bonaglia, Stefano
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Klaipėda University, Lithuania; University of Southern Denmark, Denmark.
    Active DNRA and denitrification in oxic hypereutrophic waters2021In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 194, article id 116954Article in journal (Refereed)
    Abstract [en]

    Since the start of synthetic fertilizer production more than a hundred years ago, the coastal ocean has been exposed to increasing nutrient loading, which has led to eutrophication and extensive algal blooms. Such hypereutrophic waters might harbor anaerobic nitrogen (N) cycling processes due to low-oxygen mi- croniches associated with abundant organic particles, but studies on nitrate reduction in coastal pelagic environments are scarce. Here, we report on 15 N isotope-labeling experiments, metagenome, and RT-qPCR data from a large hypereutrophic lagoon indicating that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were active processes, even though the bulk water was fully oxygenated ( > 224 μM O 2 ). DNRA in the bottom water corresponded to 83% of whole-ecosystem DNRA (water + sedi- ment), while denitrification was predominant in the sediment. Microbial taxa important for DNRA accord- ing to the metagenomic data were dominated by Bacteroidetes (genus Parabacteroides ) and Proteobac- teria (genus Wolinella ), while denitrification was mainly associated with proteobacterial genera Pseu- domonas, Achromobacter , and Brucella . The metagenomic and microscopy data suggest that these anaero- bic processes were likely occurring in low-oxygen microniches related to extensive growth of filamentous cyanobacteria, including diazotrophic Dolichospermum and non-diazotrophic Planktothrix . By summing the total nitrate fluxes through DNRA and denitrification, it results that DNRA retains approximately one fifth (19%) of the fixed N that goes through the nitrate pool. This is noteworthy as DNRA represents thus a very important recycling mechanism for fixed N, which sustains algal proliferation and leads to further enhancement of eutrophication in these endangered ecosystems.

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  • 23. Buetti-Dinh, Antoine
    et al.
    Dethlefsen, Olga
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Friedman, Ran
    Dopson, Mark
    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 IcIR 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.

  • 24.
    Callac, Nolwenn
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences. Université de Brest, France; Ifremer, France; CNRS, France.
    Oger, Philippe
    Lesongeur, Francoise
    Rattray, Jayne E.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Vannier, Pauline
    Michoud, Gregoire
    Beauverger, Mickael
    Gayet, Nicolas
    Rouxel, Olivier
    Jebbar, Mohamed
    Godfroy, Anne
    Pyrococcus kukulkanii sp nov., a hyperthermophilic, piezophilic archaeon isolated from a deep-sea hydrothermal vent2016In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 66, p. 3142-3149Article in journal (Refereed)
    Abstract [en]

    A novel hyperthermophilic, piezophilic, anaerobic archaeon, designated NCB100(T), was isolated from a hydrothermal vent flange fragment collected in the Guaymas basin at the hydrothermal vent site named 'Rebecca's Roost' at a depth of 1997 m. Enrichment and isolation were performed at 100 degrees C under atmospheric pressure. Cells of strain NCB100(T) were highly motile, irregular cocci with a diameter of -1 mu m. Growth was recorded at temperatures between 70 and 112 degrees C (optimum 105 degrees C) and hydrostatic pressures of 0.1-80 MPa (optimum 40-50 MPa). Growth was observed at pH 3.5-8.5 (optimum pH 7) and with 1.5-7% NaCl (optimum at 2.5-3 %). Strain NCB100(T) was a strictly anaerobic chemo-organoheterotroph and grew on complex proteinaceous substrates such as yeast extract, peptone and tryptone, as well as on glycogen and starch. Elemental sulfur was required for growth and was reduced to hydrogen sulfide. The fermentation products from complex proteinaceous substrates were CO2 and H-2. The G+C content of the genomic DNA was 41.3 %. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain NCB100(T) belongs to the genus Pyrococcus, showing 99% similarity with the other described species of the genus Pyrococcus. On the basis of physiological characteristics, DNA G+C content, similarity level between ribosomal proteins and an average nucleotide identity value of 79 %, strain NCB100(T) represents a novel species for which the name Pyrococcus kukulkanii sp. nov. is proposed. The type strain is NCB100(T) (=DSM 101590(T) =Souchotheque de Bretagne BG1337(T)).

  • 25.
    Capo, Eric
    et al.
    Umeå University, Sweden; SLU Uppsala, Sweden.
    Broman, Elias
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre.
    Bonaglia, Stefano
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. University of Gothenburg, Sweden.
    Bravo, Andrea G.
    Spanish National Research Council (CSIC), Spain.
    Bertilsson, Stefan
    SLU Uppsala, Sweden.
    Soerensen, Anne L.
    Swedish Museum of Natural History, Sweden.
    Pinhassi, Jarone
    Linnaeus University, Sweden.
    Lundin, Daniel
    Linnaeus University, Sweden.
    Buck, Moritz
    SLU Uppsala, Sweden.
    Hall, Per O. J.
    University of Gothenburg, Sweden.
    Nascimento, Francisco J. A.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre.
    Björn, Erik
    Umeå University, Sweden.
    Oxygen‐deficient water zones in the Baltic Sea promote uncharacterized Hg methylating microorganisms in underlying sediments2022In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 67, no 1, p. 135-146Article in journal (Refereed)
    Abstract [en]

    Human-induced expansion of oxygen-deficient zones can have dramatic impacts on marine systems and its resident biota. One example is the formation of the potent neurotoxic methylmercury (MeHg) that is mediated by microbial methylation of inorganic divalent Hg (HgII) under oxygen-deficient conditions. A negative consequence of the expansion of oxygen-deficient zones could be an increase in MeHg production due to shifts in microbial communities in favor of microorganisms methylating Hg. There is, however, limited knowledge about Hg-methylating microbes, i.e., those carrying hgc genes critical for mediating the process, from marine sediments. Here, we aim to study the presence of hgc genes and transcripts in metagenomes and metatranscriptomes from four surface sediments with contrasting concentrations of oxygen and sulfide in the Baltic Sea. We show that potential Hg methylators differed among sediments depending on redox conditions. Sediments with an oxygenated surface featured hgc-like genes and transcripts predominantly associated with uncultured Desulfobacterota (OalgD group) and Desulfobacterales (including Desulfobacula sp.) while sediments with a hypoxic-anoxic surface included hgc-carrying Verrucomicrobia, unclassified Desulfobacterales, Desulfatiglandales, and uncharacterized microbes. Our data suggest that the expansion of oxygen-deficient zones in marine systems may lead to a compositional change of Hg-methylating microbial groups in the sediments, where Hg methylators whose metabolism and biology have not yet been characterized will be promoted and expand. 

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  • 26.
    Caputo, Andrea
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Genomic and morphological diversity of marine planktonic diatom-diazotroph associations: a continuum of integration and diversification through geological time2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Symbioses between eukaryotes and nitrogen (N2)-fixing cyanobacteria (or diazotrophs) are quite common in the plankton community. A few genera of diatoms (Bacillariophyceae) such as Rhizosolenia, Hemiaulus and Chaetoceros are well known to form symbioses with the heterocystous diazotrophic cyanobacteria Richelia intracellularis and Calothrix rhizosoleniae. The latter are also called diatom-diazotroph associations, or DDAs. Up to now, the prokaryotic partners have been morphologically and genetically characterized, and the phylogenetic reconstruction of the well conserved nifH gene (encodes for the nitrogenase enzyme) placed the symbionts in 3 clusters based on their host-specificity, i.e. het-1 (Rhizosolenia-R. intracellularis), het-2 (Hemiaulus-R. intracellularis), and het-3 (Chaetoceros-C- rhizosoleniae). Conversely, the diatom-hosts, major representative of the phytoplankton community and crucial contributors to the carbon (C) biogeochemical cycle, have been understudied.

    The first aim of this thesis was to genetically and morphologically characterize the diatom-hosts, and to reconstruct the evolutionary background of the partnerships and the symbiont integration in the host. The molecular-clock analysis reconstruction showed the ancient appearance of the DDAs, and the traits characterizing the ancestors. In addition, diatom-hosts bearing internal symbionts (with more eroded draft genomes) appeared earlier than diatom-hosts with external symbionts. Finally a blast survey highlighted a broader distribution of the DDAs than expected.

    The second aim of this thesis was to compare genetic and physiological characteristics of the DDAs symbionts with the other eukaryote-diazotroph symbiosis, i.e. prymnesiophyte-UCYN-A (or Candidatus Atelocyanobacterium thalassa). The genome comparison highlighted more genes for transporters in het-3 (external symbiont) and in the UCYN-A based symbiosis, suggesting that symbiont location might be relevant also for metabolic exchanges and interactions with the host and/or environment. Moreover, a summary of methodological biases that brought to an underestimation of the DDAs is reported.

    The third aim of this thesis was to determine the distribution of the DDAs in the South Pacific Ocean using a quantitative polymerase chain reaction (qPCR) approach and to outline the environmental drivers of such distribution. Among the het-groups, het-1 was the most abundant/detected and co-occurred with the other 2 symbiotic strains, all responding similarly to the influence of abiotic factors, such as temperature and salinity (positive and negative correlation, respectively). Globally, Trichodesmium dominated the qPCR detections, followed by UCYN-B. UCYN-A phylotypes (A-1, A-2) were detected without their proposed hosts, for which new oligonucleotides were designed. The latter suggested a facultative symbiosis. Finally, microscopy observations of the het-groups highlighted a discrepancy with the qPCR counts (i.e. the former were several order of magnitudes lower), leading to the idea of developing a new approach to quantify the DDAs.  

    The fourth aim of this thesis was to develop highly specific in situ hybridization assays (CARD-FISH) to determine the presence of alternative life-stages and/or free-living partners. The new assays were applied to samples collected in the South China Sea and compared with abundance estimates from qPCR assays for the 3 symbiotic strains. Free-living cells were indeed detected along the transect, mainly at deeper depths. Free-living symbionts had two morphotypes: trichomes and single-cells. The latter were interpreted as temporary life-stages. Consistent co-occurrence of the 3 het-groups was also found in the SCS and application of a SEM model predicted positive interactions between the het groups. We interpreted the positive interaction as absence of intra-specific competition, and consistent with the previous study, temperature and salinity were predicted as major drivers of the DDAs distribution.

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  • 27.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Ahn, Seung-Joon
    Vogel, Heiko
    Heckel, David G.
    Transcriptional responses underlying the hormetic and detrimental effects of the plant secondary metabolite gossypol on the generalist herbivore Helicoverpa armigera2011In: BMC Genomics, E-ISSN 1471-2164, Vol. 12, p. 575-Article in journal (Refereed)
    Abstract [en]

    Background: Hormesis is a biphasic biological response characterized by the stimulatory effect at relatively low amounts of chemical compounds which are otherwise detrimental at higher concentrations. A hormetic response in larval growth rates has been observed in cotton-feeding insects in response to increasing concentrations of gossypol, a toxic metabolite found in the pigment glands of some plants in the family Malvaceae. We investigated the developmental effect of gossypol in the cotton bollworm, Helicoverpa armigera, an important heliothine pest species, by exposing larvae to different doses of this metabolite in their diet. In addition, we sought to determine the underlying transcriptional responses to different gossypol doses. Results: Larval weight gain, pupal weight and larval development time were measured in feeding experiments and a hormetic response was seen for the first two characters. On the basis of net larval weight gain responses to gossypol, three concentrations (0%, 0.016% and 0.16%) were selected for transcript profiling in the gut and the rest of the body in a two-color double reference design microarray experiment. Hormesis could be observed at the transcript level, since at the low gossypol dose, genes involved in energy acquisition such as beta-fructofuranosidases were up-regulated in the gut, and genes involved in cell adhesion were down-regulated in the body. Genes with products predicted to be integral to the membrane or associated with the proteasome core complex were significantly affected by the detrimental dose treatment in the body. Oxidoreductase activity-related genes were observed to be significantly altered in both tissues at the highest gossypol dose. Conclusions: This study represents the first transcriptional profiling approach investigating the effects of different concentrations of gossypol in a lepidopteran species. H. armigera's transcriptional response to gossypol feeding is tissue-and dose-dependent and involves diverse detoxifying mechanisms not only to alleviate direct effects of gossypol but also indirect damage such as pH disturbance and oxygen radical formation. Genes discovered through this transcriptional approach may be additional candidates for understanding gossypol detoxification and coping with gossypol-induced stress. In a generalist herbivore that has evolved transcriptionally-regulated responses to a variety of different plant compounds, hormesis may be due to a lower induction threshold of growth-promoting, stress-coping responses and a higher induction threshold of detoxification pathways that are costly and cause collateral damage to the cell.

  • 28.
    Chen, Yunying
    et al.
    Karolinska Institutet.
    Wermeling, Fredrik
    Karolinska Institutet.
    Sundqvist, Johanna
    Karolinska Institutet.
    Jonsson, Ann-Beth
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Tryggvason, Karl
    Karolinska Institutet.
    Pikkarainen, Timo
    Karolinska Institutet.
    Karlsson, Mikael C I
    Karolinska Institutet.
    A regulatory role for macrophage class A scavenger receptors in TLR4-mediated LPS responses.2010In: European Journal of Immunology, ISSN 0014-2980, E-ISSN 1521-4141, Vol. 40, no 5, p. 1451-60Article in journal (Refereed)
    Abstract [en]

    Recognition of microbial components by TLR, key sensors of infection, leads to induction of inflammatory responses. We found that, in vivo, TLR4 engagement by LPS induces up-regulation of the class A scavenger receptors (SR) macrophage receptor with a collagenous structure (MARCO) and SR-A, which occurs, at least in the case of MARCO, via both MyD88-dependent and -independent pathways. When challenging mice with a low dose of LPS followed by a high dose, class A SR-deficient mice showed a higher survival rate than WT mice. This was paired with increased production of IL-10 and anti-LPS Ab, as well as increased activation status of marginal zone B cells. However, the receptors were not crucial for survival when challenging mice i.p. with Neisseria meningitidis or Listeria monocytogenes, but they were found to contribute to microbial capture and clearance. This indicates physiological significance for the up-regulation of class A SR during early stages of bacterial infection. Thus, we believe that we have revealed a mechanism where SR regulate the activation status of the immune system and are involved in balancing a proper immune response to infection. This regulation could also be important in maintaining tolerance since these receptors have been shown to be involved in regulation of self-reactivity.

  • 29.
    Dahlgren, Ann
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Function and regulation of release factor one in Escherichia coli2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    During translation termination the stop codons UAA and UAG are recognised by release factor one (RF1). RF1 binds to the ribosome and mediates the hydrolysis of the nascent peptide from the peptidyl-tRNA. In this process, RF1 interacts directly or indirectly with several ribosomal proteins (r-proteins). To study this interaction in vivo we have used a mutant allele of RF1, prfA1. The mutation causes a temperature sensitive (Ts) phenotype and increased readthrough of the stop codons. A mutant form of r-protein S4 that suppresses this Ts phenotype was isolated. The S4 mutant also increases the readtrough of UAG caused by prfA1. In the mutated S4 allele, rpsD101, Tyr51 is changed to Asp. That change introduces a negatively charged amino acid in a part of S4 that belongs to the positively charged RNA binding surface. This might affect the binding of S4 to the 16S rRNA, to another r-protein, or to RF1, and in that way influence on the function of RF1.

    One of the few things known about the regulation of RF1 is that expression is decreased with increasing generation time. prfA is the second gene in the hemA-operon located at 27 minutes on the E. coli chromosomal map. We have shown that the growth rate regulation of RF1 is exerted at one of the promoters preceding the hemA gene, PhemA1. The promoter is also growth phase regulated and it is turned off in stationary phase. We have characterised two mutations, asuA1 and asuA2, that increase expression of RF1. The asuA2 mutation is a G to A change one nucleotide downstream of the -10 region of PhemA1. Besides increasing expression of RF1 this mutation also abolishes the growth rate and growth phase regulations we have found. The growth phase regulation is partly dependent on ppGpp. We present two models concerning the effect of ppGpp on PhemA1, and what the asuA2 mutation does to it. The prfA gene has low translation initiation efficiency due to a long spacing between the Shine-Dalgarno (SD) sequence and the start codon. The asuA1 mutation creates a new start codon with a shorter distance to the SD sequence. Most likely this increases the efficiency of translation initiation. That PhemA1 is turned off in stationary phase suggests additional regulation of RF1. Our results indicate a putative promoter for the prfA gene within hemA. This promoter does not seem to be growth rate or growth phase regulated.

  • 30.
    de Klerk, Nele
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Host-bacteria interactions: Host cell responses and bacterial pathogenesis2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Helicobacter pylori colonizes the human stomach, where it causes gastritis that may develop into peptic ulcer disease or cancer when left untreated. Neisseria gonorrhoeae colonizes the urogenital tract and causes the sexually transmitted disease gonorrhea. In contrast, Lactobacillus species are part of the human microbiota, which is the resident microbial community, and are considered to be beneficial for health. The first host cell types that bacteria encounter when they enter the body are epithelial cells, which form the border between the inside and the outside, and macrophages, which are immune cells that engulf unwanted material.      

    The focus of this thesis has been the interaction between the host and bacteria, aiming to increase our knowledge of the molecular mechanisms that underlie the host responses and their effects on bacterial pathogenicity. Understanding the interactions between bacteria and the host will hopefully enable the development of new strategies for the treatment of infectious disease.

    In paper I, we investigated the effect of N. gonorrhoeae on the growth factor amphiregulin in cervical epithelial cells and found that the processing and release of amphiregulin changes upon infection. In paper II, we examined the expression of the transcription factor early growth response-1 (EGR1) in epithelial cells during bacterial colonization. We demonstrated that EGR1 is rapidly upregulated by many different bacteria. This upregulation is independent of the pathogenicity, Gram-staining type and level of adherence of the bacteria, but generally requires viable bacteria and contact with the host cell. The induction of EGR1 is mediated primarily by signaling through EGFR, ERK1/2 and β1-integrins. In paper III, we described the interactions of the uncharacterized protein JHP0290, which is secreted by H. pylori, with host cells. JHP0290 is able to bind to several cell types and induces apoptosis and TNF release in macrophages. For both of these responses, signaling through Src family kinases and ERK is essential. Apoptosis is partially mediated by TNF release. Finally, in paper IV, we showed that certain Lactobacillus strains can reduce the colonization of H. pylori on gastric epithelial cells. Lactobacilli decrease the gene expression of SabA and thereby inhibit the binding mediated by this adhesin.

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  • 31.
    Diez, Beatriz
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Pedros-Alio, Carlos
    Anto, Meritxell
    Snoeijs, Pauline
    Stockholm University, Faculty of Science, Department of Systems Ecology.
    High cyanobacterial nifh gene diversity in arctic seawater and sea ice brine2012In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 4, no 3, p. 360-366Article in journal (Refereed)
    Abstract [en]

    Although cyanobacterial diazotrophs are common in Arctic terrestrial and freshwater habitats, they have been assumed to be absent from Arctic marine habitats. We report here a high diversity of cyanobacterial nifH genes in Fram Strait and the Greenland Sea. The nifH gene encodes the iron protein of the nitrogenase enzyme complex, which is essential for biological N2 fixation. Using primers specific for nifH genes we uncovered communities of autotrophic and heterotrophic bacteria in sea ice brine and seawater between latitudes 65 and 81 degrees N. Cyanobacteria (Oscillatoriales and Chroococcales) with known marine planktonic and benthic distributions were distinguished, alongside a mix of metabolically versatile eubacteria (nifH Clusters I and III). Using primers selective for cyanobacterial nifH genes we identified filamentous non-heterocystous Trichodesmium-like and LPP (Leptolyngbya, Phormidium and Plectonema)-like Oscillatoriales, as well as Cyanothece-like Chroococcales in a brine sample from 81 degrees N. The occurrence of Trichodesmium-like cyanobacteria was further confirmed by sequences of the hetR gene of Trichodesmium. Microscopic examinations confirmed the presence of viable filamentous and unicellular cyanobacteria. Our results reveal the potential for microbial N2 fixation in the Arctic seas. However, it is still left to determine if these genes are also metabolically active before any biogeochemical importance of diazotrophy in the polar oceans can be assessed.

  • 32. Dominguez-Escobar, Julia
    et al.
    Beltran, Yislem
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Diez, Beatriz
    Stockholm University, Faculty of Science, Department of Botany.
    Ininbergs, Karolina
    Stockholm University, Faculty of Science, Department of Botany.
    Souza, Valeria
    Falcon, Luisa I.
    Phylogenetic and molecular clock inferences of cyanobacterial strains within Rivulariaceae from distant environments2011In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 316, no 2, p. 90-99Article in journal (Refereed)
    Abstract [en]

    Heterocyst-forming cyanobacteria are important players at both evolutionary and ecological scales, but to date it has been difficult to establish their phylogenetic affiliations. We present data from a phylogenetic and molecular clock analysis of heterocystous cyanobacteria within the family Rivulariaceae, including the genera Calothrix, Rivularia, Gloeotrichia and Tolypothrix. The strains were isolated from distant geographic regions including fresh and brackish water bodies, microbial mats from beach rock, microbialites, pebble beaches, plus PCC strains 7103 and 7504. Phylogenetic inferences (distance, likelihood and Bayesian) suggested the monophyly of genera Calothrix and Rivularia. Molecular clock estimates indicate that Calothrix and Rivularia originated similar to 1500 million years ago (MYA) ago and species date back to 400-300 MYA while Tolypothrix and Gloeotrichia are younger genera (600-400 MYA).

  • 33.
    D'Onofrio, Cladio
    et al.
    University of Pisa, Italy.
    Lindberg, Sylvia
    Stockholm University, Faculty of Science, Department of Botany.
    Sodium induces simultaneous changes in cytosolic calcium and pH in salt-tolerant quince protoplasts2009In: Journal of plant physiology (Print), ISSN 0176-1617, E-ISSN 1618-1328, Vol. 166, p. 1755-1763Article in journal (Refereed)
    Abstract [en]

    Previousexperimentswithsalt-resistantquinceBA29(Cydonia oblonga cv.Mill.) have shownthatthiscultivartakesupsodiumtransientlyintothecytosolofshoot protoplasts onlyintheabsenceofcalciumchloride,orat o1mMcalciumchloride. Addition ofNaClZ100mMtosingleprotoplastsfrom in vitro-cultivated quinceinthe presence of1.0mMcalciuminducedinstantchangesinthecytosolicconcentrations of calciumandprotons.Thesechangeswereinvestigatedbyuseoftetra [acetoxymethyl] estersofthefluorescentstilbenechromophoresFura2andbis- carboxyethyl-carboxyfluorescein (BCECF),respectively.ThecytosolicCa2+ dynamics in theprotoplastsweredependentontheconcentrationofNaCladded.Thechanges in calciumdifferedinamplitudeandfinalconcentrationandwerecorrelatedintime mainly withchangesinpH.Additionof100–400mMNaCltotheprotoplastscausedan oscillating increaseinthecytosoliclevelofcalcium,andthenadecrease.Addition of mannitol,ofequiosmolarconcentrationtoNaCl,didnotincreasethecytosolic calcium concentration.Moreover,therewasnoincreaseincytosoliccalciumwhen NaCl wasaddedinthepresenceofcalciumbindingethyleneglycol-bis(beta- aminoethylether)-N,N,N0,N0-tetra aceticacid(EGTA),orlantanorverapamil,two inhibitors ofplasmamembranecalciumchannels.Therefore,weconcludethat,in salt-resistant quince,sodiuminducesaninfluxofcalciumintothecytosolbyplasma membrane calciumchannels,andasimultaneousincreaseincytosolicpH.Because these changeswereobtainedinthepresenceof1mMcalciuminthemedium,they were notduetosodiumuptakeintothecytosol.

  • 34.
    Dou, Dan
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Influenza A Virus: Spatial analysis of influenza genome trafficking and the evolution of the neuraminidase protein2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Influenza A viruses (IAVs) are a common infectious agent that seasonally circulates within the human population that causes mild to severe acute respiratory infections. The severity of the infection is often related to how the virus has evolved with respect to the pre-existing immunity in the population. For IAVs, the most common mechanisms to avoid the immune response are to vary the surface antigens, hemagglutinin (HA) and neuraminidase (NA), by processes known as antigenic drift and shift.

    Antigenic drift refers to point mutations that accumulate in HA and NA as a result of the antibody-mediated selection pressure that exists in the population. The majority of the changes attributed to antigenic drift localize to HA and NA surface exposed regions, however this does not exclude that drift can also result in the selection of residues that are not exposed. One region where non-exposed residues have potentially been selected for is the NA transmembrane domain (TMD) of human H1N1 IAVs, where a temporal bias exists for the accumulation of polar residues. By examining these sequence changes in the NA TMD, we found that the polar residues contribute to the amphipathic characteristic of the NA TMD, which mediates the oligomerization of the N-terminus. As more polar residues became incorporated, the strength of the TMD-TMD interaction increased, presumably to benefit the NA head domain assembly into a functional tetramer. We determined that the amphiphilic drift in the NA TMD is able to bypass the strict hydrophobicity required for membrane insertion at the endoplasmic reticulum because it can utilize the co-translational translocation process to facilitate the insertion and inversion of its non-ideal TMD. The contribution of the TMD to proper NA assembly was traced to the formation of the Ca2+ binding pocket that is located at the center of the tetrameric assembly, as this pocket lies above the stalk linker regions and must be occupied for NA to function.

    In addition to antigenic drift, NA and HA can also undergo antigenic shift. Antigenic shift occurs when either of the gene segments encoding NA or HA are exchanged with ones from another IAV encoding another subtype of NA or HA. Different from antigenic drift, antigenic shift can only occur when a cell is co-infected and most investigations on the process of reassortment have been made at the protein level due to the methodological issues for labeling the RNA genome in situ. To overcome these technical limitations, we developed an in situ RNA labeling approach that provides highly specific spatial resolution of the IAV genome throughout the infection process. By applying this approach to temporally analyze the co-infection process, we found that the entry of a second IAV is stalled in the cytoplasm if another IAV has begun to replicate. Together, these results provide insight into the low frequency of antigenic shift in nature and provide evidence that non-exposed residues may make an underappreciated contribution to NA antigenic drift in human H1N1 viruses.

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  • 35. Downing, Simone
    et al.
    Scott, Laura Louise
    Zguna, Nadezda
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Downing, Timothy Grant
    Human Scalp Hair as an Indicator of Exposure to the Environmental Toxin -N-Methylamino-l-alanine2018In: Toxins, ISSN 2072-6651, E-ISSN 2072-6651, Vol. 10, no 1, article id 14Article in journal (Refereed)
    Abstract [en]

    Dietary or aerosol exposure to the environmental neurotoxin -N-methylamino-l-alanine (BMAA) is a putative risk factor for the development of sporadic neurodegenerative disease. There are many potential sources of BMAA in the environment, but BMAA presence and quantities are highly variable. It has been suggested that BMAA in human hair may serve as an indicator of exposure. We sought to evaluate the use of the BMAA content of human scalp hair as an indicator of exposure, as well as the correlation between specific lifestyle or dietary habits, reported as hypothesised exposure risk factors, and BMAA in hair. Scalp hair samples and questionnaires were collected from participants in a small residential village surrounding a freshwater impoundment renowned for toxic cyanobacterial blooms. Data suggested a positive correlation between hair BMAA content and consumption of shellfish, and possibly pork. No statistically significant correlations were observed between hair BMAA content and residential proximity to the water or any other variable. Hair BMAA content was highly variable, and in terms of exposure, probably reflects primarily dietary exposure. However, the BMAA content of human hair may be affected to a great extent by several other factors, and as such, should be used with caution when evaluating human BMAA exposure, or correlating exposure to neurodegenerative disease incidence.

  • 36.
    Dziedziech, Alexis
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Timing Matters: Wounding and entomopathogenic nematode infection kinetics2021Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Over time, insects have developed complex strategies to defend themselves against presenting threats. However, in the evolutionary arms race of survival, pathogens have adapted to quickly overcome the immune response mounted by the host. In this thesis, we assess how quickly entomopathogenic nematodes (EPNs) can overcome the host, Drosophila melanogaster. We then look at the clotting reaction at a hypothetical point of entry for the nematode and bring resolution to the order of protein interaction focusing on three proteins important in the anti-nematode defense. Finally, we look closer into detail at how crystal cells secrete one of those proteins, prophenoloxidase (PPOII) using a mode of programmed cell death. 

    (Paper I) In the course of EPN infection, little was known about how quickly the worms can overcome the host immune system. Here we found that after penetrating the host, EPNs cause septicemia within 4 to 6 hours. (Paper II) Three proteins, Glutactin (Glt), Transglutaminase (Tg), and PPOII have been found to be important in the anti-nematode response. Here we created GFP-tagged fly constructs to follow their role in clot formation. In early clot formation, Tg was immediately secreted from hemocytes though it was localized around the cell membrane, Glt then entered clot fibers followed by PPOII which acted in late clot formation. (Paper III) Here we looked closer into Tg and PPOII secretion variability. PPOII from immature, but not mature crystal cells colocalized with a membrane marker. Tg, when driven with a pan tissue driver, was found located in clotting fibers, in contrast with paper II. (Paper IV) In an in vivo immune scenario, crystal cells were recruited to the wound site and burst rapidly in a caspase-dependent manner. We demonstrate that the mode of programmed cell death, pyroptosis, exists in Drosophila by way of convergent evolution.

    This thesis brings to light the variation found within the infection process for EPNs as well as the clotting response based on larval age, tissue type, and the maturity of a single cell type. Timing in each of these immune scenarios can give very different indications about the kind of immune response mounted and even the role of an individual cell.

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    Timing Matters: Wounding and entomopathogenic nematode infection kinetics
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  • 37.
    Díez, Beatriz
    et al.
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Pontificia Universidad Católica de Chile, Chile; Center for Climate Change and Resilience Research (CR)2, Chile.
    Nylander, Johan A. A.
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Swedish Museum of Natural History, Sweden.
    Ininbergs, Karolina
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Dupont, Christopher L.
    Allen, Andrew E.
    Yooseph, Shibu
    Rusch, Douglas B.
    Bergman, Birgitta
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution2016In: PLOS ONE, E-ISSN 1932-6203, Vol. 11, no 5, article id e0155757Article in journal (Refereed)
    Abstract [en]

    Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 mu m to 20 mu m and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial lightharvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.

  • 38.
    Edberg, Frida
    et al.
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Andersson, Anders F.
    Holmström, Sara J. M.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Bacterial community composition in the water column of a lake formed by a former uranium open pit mine2012In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 64, no 4, p. 870-880Article in journal (Refereed)
    Abstract [en]

    Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (similar to 20 years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40 % of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.

  • 39. Ellenbogen, Jared B.
    et al.
    Borton, Mikayla A.
    McGivern, Bridget B.
    Cronin, Dylan R.
    Hoyt, David W.
    Freire-Zapata, Viviana
    McCalley, Carmody K.
    Varner, Ruth K.
    Crill, Patrick M.
    Stockholm University, Faculty of Science, Department of Geological Sciences. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Wehr, Richard A.
    Chanton, Jeffrey P.
    Woodcroft, Ben J.
    Tfaily, Malak M.
    Tyson, Gene W.
    Rich, Virginia I.
    Wrighton, Kelly C.
    Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost2023In: mSystems, E-ISSN 2379-5077Article in journal (Refereed)
    Abstract [en]

    While wetlands are major sources of biogenic methane (CH4), our understanding of resident microbial metabolism is incomplete, which compromises the prediction of CH4 emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire in Arctic Sweden. In quadrupling the genomic representation of the site’s methanogens and examining their encoded metabolism, we revealed that nearly 20% of the metagenome-assembled genomes (MAGs) encoded the potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; for Methanosarcinales and Methanobacteriales MAGs, these data indicated the use of methylated oxygen compounds (e.g., methanol), while for Methanomassiliicoccales, they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1,700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activities. Methanogenesis across increasing permafrost thaw is thus revised from the sole dominance of hydrogenotrophic production and the appearance of acetoclastic at full thaw to consider the co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.

  • 40.
    Envall, Ida
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Gustavsson, Lena M.
    Swedish Museum of Natural History.
    Erséus, Christer
    University of Gothenburg.
    Genetic and morphological variation in “cosmopolitan” Nais worms (Annelida, Clitellata, Naididae): species diversity beyond that of current taxonomyManuscript (Other academic)
  • 41.
    Eriksson, Harald
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Berta, David
    Örmälä-Odegrip, Anni-Maria
    Giske, Christian G.
    Nilsson, Anders S.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    A novel phage cocktail inhibiting the growth of 99 β-lactamase carrying Klebsiella pneumoniae clinical isolates in vitroManuscript (preprint) (Other academic)
    Abstract [en]

    Klebsiella pneumoniae is a gram-negative bacterial pathogen, accountable for a variety of nosocomial infections in immunocompromised patients, open-wound infections and community-acquired pneumonia in elderly. K. pneumoniae strains harboring plasmid-mediated extended spectrum β-lactamase enzymes (ESBL) are resistant to all penicillin and cephalosoprins, whereas bacteria capable of producing carbapenemase enzymes (e.g. NDM, KPC and VIM) are resistant to virtually all β-lactam group antibiotics. The use of bacterial viruses lysing bacterial hosts (phage therapy) has been suggested as an alternative in fighting bacterial infections resistant to known antibiotics. In this study, we assembled a phage cocktail consisting of 6 novel lytic bacteriophages infecting K. pneumoniae. The phage cocktail was tested against 125 β-lactamase producing clinical isolates of K. pneumoniae and we found that at high titres, the cocktail was able to lyse 99 of these isolates in vitro.

  • 42.
    Eriksson, Jens
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Virulence Factors and Motility Mechanisms of Pathogenic Neisseria2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Neisseria gonorrhoeae and Neisseria meningitidis are two closely related human specific pathogens. Neisseria gonorrhoeae is the causative agent for the sexually transmitted disease gonorrhea and often causes asymptomatic infections in women which is a cause of infertility. Neisseria meningitidis is a major cause of mortality world-wide through bacterial meningitis and septicemia. The severity of meningococcal disease, especially in sub-Saharan Africa warrants development of effective vaccines against serogroups that currently lack them. Here, Neisseria host-pathogen interactions and common virulence factors that may prove useful in vaccine development and in understanding disease caused by pathogenic Neisseria are reviewed and investigated. The aim of this thesis is to investigate the virulence-associated properties of the universally expressed N. meningitidis proteins NhhA, NafA, PilU and PilT, as well as to characterize the twitching motility of the pathogenic Neisseria. The conserved autotransporter adhesin NhhA has in Paper I of this thesis been investigated in a murine model of meningococcemia and found to be important for intranasal colonization and disease outcome of N. meningitidis in CD46 transgenic mice. NafA has in Paper II of this thesis been named and identified as a novel anti-aggregation factor that impacts both pilus bundling and the virulence potential of N. meningitidis. The ATPases, PilU and PilT, which are involved in the functionality of pili were studied in Paper III of this thesis. PilU and PilT were found to modulate Neisseria microcolony formation, host cell adhesion, pilus retraction, serum resistance, as well as mortality in a mouse model of meningococcal disease. Finally, Paper IV of this thesis also provides novel insights into the nature of twitching motility in pathogenic Neisseria. By live-cell microscopy and automated particle tracking coupled with visualization of pili in motile bacteria we found that N. meningitidis strains, on average, move faster and utilizes more pili then N. gonorrhoeae. In summary, this thesis investigates Neisseria virulence factors in general, type IV pili in particular and characterizes the roles of several virulence-associated proteins and twitching motility in the pathogenic Neisseria.

  • 43.
    Eriksson, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Eriksson, Olaspers Sara
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Maudsdotter, Lisa
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Palm, Oskar
    Institutionen för teoretisk fysik, KTH.
    Sarkissian, Tim
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Aro, Helena
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Wallin, Mats
    Institutionen för teoretisk fysik, KTH.
    Jonsson, Ann-Beth
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Characterization of motility and piliation in pathogenic NeisseriaManuscript (preprint) (Other academic)
  • 44.
    Eriksson, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Eriksson, Olaspers Sara
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Palm, Oscar
    KTH.
    Sarkissian, Tim
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Wallin, Mats
    KTH.
    Jonsson, Ann-beth
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Difference in twitching motility between Neisseria meningitidis and Neisseria gonorrhoeae and its relation to pilus dynamicsManuscript (preprint) (Other academic)
    Abstract [en]

    Type IV pili of pathogenic Neisseria, i. e. Neisseria gonorrhoeae and Neisseria meningitidis, are essential for initial attachment to host cells, induction of signal transduction cascades and disease development. A characteristic feature of type IV pili is their ability to retract, which generates forces that move bacteria over surfaces. However, the relation between bacterial motility and pilus dynamics remains poorly understood. In this work we analyzed bacterial motility and monitored movement of fluorescently labeled pili by live cell imaging. We found that movement of N. meningitidis occurred at higher speed and with a larger number of retracting pili than for N. gonorrhoeae. Analysis of time-lapse images suggested that N. gonorrhoeae most often moved using one retracting pilus, whereas N. meningitidis most often used four pili. There were no differences in the membrane distribution of PilT among strains. However, we found significantly higher levels of PilT in N. gonorrhoeae than in N. meningitidis. This produces a higher retraction probability, which could contribute to explaining the lower number of pili observed in N. gonorrhoeae. Finally, we propose a mechanism for how the speed of bacterial movement on a surface depends on the number of retracting pili.

  • 45.
    Eriksson, Olaspers Sara
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Pathogenic Neisseria: Single cell motility, multicellular dynamics and antimicrobial susceptibility2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Neisseria meningitidis and Neisseria gonorrhoeae can colonize humans without causing any symptoms. However, gonorrhea and invasive meningococcal disease are serious health concerns. An essential virulence factor for neisserial adhesion to host cells, twitching motility and microcolony formation/aggregation is the retractile type IV pili (Tfp). The scope of this thesis stretches from the motility of single Neisseria cells, via the multicellular dynamics of N. meningitidis microcolonies, to the bactericidal and endotoxin-inhibiting activity of a novel anti-meningococcal peptide. The Tfp machinery in pathogenic Neisseria is highly conserved. Nevertheless, our data demonstrate species-specific expression levels of the Tfp retraction ATPase PilT. By using live-cell microscopy and particle tracking together with visualization of pili, differences between N. gonorrhoeae and N. meningitidis were also observed in piliation and twitching motility speed. However, these differences could not be attributed to the contrasting PilT expressions per se (Paper I). The importance of PilT for pilus dynamics is well established in the literature while comprehensive knowledge of the paralog PilU is lacking. In Paper II, results suggest that PilU promotes timely formation of microcolonies. Furthermore, both PilU and PilT were required for full virulence of meningococci in vivo. The meningococcal response upon adhesion to host cells includes upregulation of the novel virulence factor Neisseria anti-aggregation factor A (NafA). Our data indicate that NafA limits microcolony formation by preventing excessive formation of Tfp bundles (Paper III). Microcolony dispersal is a prerequisite for close adhesion and mucosal invasion. Dispersal progressed rapidly on host cells and upon induction with host cell-conditioned medium (Paper IV). The dispersal phase was not altered in NafA-deficient meningococci. However, NafA may be important after microcolony dispersal on host cells for maintaining bacteria in a single cell state (Paper IV). In Paper V, a screen of cell-penetrating peptides for antimicrobial activity towards meningococci demonstrated that transportan-10 (TP10) exhibited rapid membrane-disruptive and bactericidal activity. TP10 also decreased bacteraemia levels in a murine model of meningococcal disease. Furthermore, TP10 reduced the proinflammatory effect of endotoxin on macrophages. Thus, TP10 displays two properties that may be utilized for the development of a peptide-based treatment against pathogens.

  • 46.
    Eriksson, Olaspers Sara
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Sigurlásdóttir, Sara
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Jonsson, Ann-Beth
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    A host cell-derived factor induces the dispersal of Neisseria meningitidis microcoloniesManuscript (preprint) (Other academic)
  • 47. Erttmann, Saskia F.
    et al.
    Gekara, Nelson O.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. University of Freiburg, Germany.
    Protocol for isolation of microbiota-derived membrane vesicles from mouse blood and colon2023In: STAR Protocols, ISSN 2666-1667, Vol. 4, no 1, article id 102046Article in journal (Refereed)
    Abstract [en]

    Bacterial membrane vesicles have emerged as gadgets allowing remote communication between the microbiota and distal host organs. Here we describe a protocol for enriching vesicles from serum and colon that could widely be adapted for other tissues. We detail pre-clearing of serum or colon fluids using 0.2-μm syringe filters and their concentration by centrifugal filter devices. We also describe vesicle isolation with qEV size exclusion columns and finally the concentration of isolated vesicle fractions for downstream analyses.

  • 48.
    Fagundes Macedo, Diego
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. University of Ostrava, Czech Republic.
    Grybchuk, Danyil
    Reznarova, Jana
    Votypka, Jan
    Klocek, Donnamae
    Yurchenko, Tatiana
    Sevcik, Jan
    Magri, Alice
    Dolinska, Michaela Urda
    Zahonova, Kristina
    Lukes, Julius
    Serviene, Elena
    Jaszayova, Alexandra
    Serva, Saulius
    Malysheva, Marina N.
    Frolov, Alexander O.
    Yurchenko, Vyacheslav
    Kostygov, Alexei Yu.
    Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris2023In: BMC Biology, E-ISSN 1741-7007, Vol. 21, no 1, article id 191Article in journal (Refereed)
    Abstract [en]

    Background Trypanosomatids are parasitic flagellates well known because of some representatives infecting humans, domestic animals, and cultural plants. Many trypanosomatid species bear RNA viruses, which, in the case of human pathogens Leishmania spp., influence the course of the disease. One of the close relatives of leishmaniae, Leptomonas pyrrhocoris, has been previously shown to harbor viruses of the groups not documented in other trypanosomatids. At the same time, this species has a worldwide distribution and high prevalence in the natural populations of its cosmopolitan firebug host. It therefore represents an attractive model to study the diversity of RNA viruses.Results We surveyed 106 axenic cultures of L. pyrrhocoris and found that 64 (60%) of these displayed 2-12 double-stranded RNA fragments. The analysis of next-generation sequencing data revealed four viral groups with seven species, of which up to five were simultaneously detected in a single trypanosomatid isolate. Only two of these species, a tombus-like virus and an Ostravirus, were earlier documented in L. pyrrhocoris. In addition, there were four new species of Leishbuviridae, the family encompassing trypanosomatid-specific viruses, and a new species of Qinviridae, the family previously known only from metatranscriptomes of invertebrates. Currently, this is the only qinvirus with an unambiguously determined host. Our phylogenetic inferences suggest reassortment in the tombus-like virus owing to the interaction of different trypanosomatid strains. Two of the new Leishbuviridae members branch early on the phylogenetic tree of this family and display intermediate stages of genomic segment reduction between insect Phenuiviridae and crown Leishbuviridae.Conclusions The unprecedented wide range of viruses in one protist species and the simultaneous presence of up to five viral species in a single Leptomonas pyrrhocoris isolate indicate the uniqueness of this flagellate. This is likely determined by the peculiarity of its firebug host, a highly abundant cosmopolitan species with several habits ensuring wide distribution and profuseness of L. pyrrhocoris, as well as its exposure to a wider spectrum of viruses compared to other trypanosomatids combined with a limited ability to transmit these viruses to its relatives. Thus, L. pyrrhocoris represents a suitable model to study the adoption of new viruses and their relationships with a protist host.

  • 49. Falcon, Luisa I
    et al.
    Lindwall, Susanne
    Stockholm University, Faculty of Science, Department of Botany. Växtfysiologi.
    Bauer, Karolina
    Stockholm University, Faculty of Science, Department of Botany. Växtfysiologi.
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany. Växtfysiologi.
    Carpenter, Edward C
    Ultrastructure of unicellular N-2 fixing cyanobacteria from the tropical North Atlantic and subtropical North Pacific Oceans2004In: Journal of Phycology, Vol. 40, no 6, p. 1074-1078Article in journal (Refereed)
    Abstract [en]

    Abstract: Nitrogen fixing unicellular marine cyanobacteria may have a major role in the global biogeochemistry of N; nevertheless, little is known about their phylogeny and morphology. We isolated N-2 fixing unicellular cyanobacteria from the tropical North Atlantic and subtropical North Pacific Oceans and examined ultrastructural dynamics during dark:light cycles when grown in incubators. The isolate from the subtropical North Pacific was larger and showed a size variation from 3 to 7 mum but had similar morphology and cell division-plane characteristics as the isolate from the North Atlantic (2.5 mum). Nitrogen fixation only occurred during the dark phase, and ultrastructural analysis demonstrated changes in the appearance and quantity of large carbohydrate-like granules present in the cells. To verify the composition of these carbohydrate-like granules, staining with periodic acid, thioacetic acid, and silver was carried out, and a positive reaction was obvious in all cells. The cells from the Atlantic seemed to empty their polysaccharide granules during the night, whereas those from the Pacific showed a decrease in the number of their granules. Our work suggests that phylogenetically related strains of unicellular N-2 fixing cyanobacteria from different oceans showed similar carbohydrate-like granules that could be used to fuel N-2 fixation during darkness.

  • 50.
    Faxén, Margareta
    Stockholm University, Faculty of Science, Department of Microbiology.
    Studies of translation in E. coli1993Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A cis-acting translational mutation in the beginning of the glnS gene was analyzed; this mutation creates a extra base pair to a proposed extended ribosome binding site. When increasing the complementarity to this extended ribosome binding site, it was demonstrated that the expression increased; correspondingly, when complementarity was decreasd the expression went down. It was also shown that the presence of rare codons near the beginning of the gene can affect expression.

    Studies of a S13 mutant (rpsM413) revealed that the mutant allele is associated with slow growth rate and slow elongation rate. The 30S subunit showed a reduced sedimentation coefficient but was able to form apparently normal 70S ribosomes.

    Investigations to see whether ribosomal mutants are able to affect proofreading in vivo found that the missense and nonsense suppressors are affected by rpsD mutations in a rather unpredictable manner. It was shown that the ribosome allele, the nature of the suppressor tRNA, the codon context, and the structure of the anticodon loop are the determinig factors. rpsL mutations decrease the nonsense suppression, in accordance with their restrictive effect on translational error formation.

    Streptomycin, which is known to increase translational error in vitro, did not increase efficiency of nonsense suppressor tRNAs in strains with normal or rpsL ribosomes. It did so only in combination with one rpsL mutation which is associated with streptomycin pseudodependence.

    The presence or absence of the modification ms2i6A37 in the tRNA was found to be a determining factor in the functional response to the ribosomal mutations. These effects strongly indicate that tRNA is directly involved in this phenomena.

    The role of ppGpp was investigated, and the results suggest that it affects transcription efficiency, but not translation. ppGpp seems to play a role in the tuning of the coupling between transcription and translation.

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