| 1. |
- Caputo, Andrea, 1988-
(författare)
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Genomic and morphological diversity of marine planktonic diatom-diazotroph associations : a continuum of integration and diversification through geological time
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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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| 2. |
- Ariöz, Candan, 1983-
(författare)
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Exploring the Interplay of Lipids and Membrane Proteins
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The interplay between lipids and membrane proteins is known to affect membrane protein topology and thus have significant effect (control) on their functions. In this PhD thesis, the influence of lipids on the membrane protein function was studied using three different membrane protein models.A monotopic membrane protein, monoglucosyldiacylglyecerol synthase (MGS) from Acholeplasma laidlawii is known to induce intracellular vesicles when expressed in Escherichia coli. The mechanism leading to this unusual phenomenon was investigated by various biochemical and biophysical techniques. The results indicated a doubling of lipid synthesis in the cell, which was triggered by the selective binding of MGS to anionic lipids. Multivariate data analysis revealed a good correlation with MGS production. Furthermore, preferential anionic lipid sequestering by MGS was shown to induce a different fatty acid modeling of E. coli membranes. The roles of specific lipid binding and the probable mechanism leading to intracellular vesicle formation were also investigated.As a second model, a MGS homolog from Synechocystis sp. PCC6803 was selected. MgdA is an integral membrane protein with multiple transmembrane helices and a unique membrane topology. The influence of different type of lipids on MgdA activity was tested with different membrane fractions of Synechocystis. Results indicated a very distinct profile compared to Acholeplasma laidlawii MGS. SQDG, an anionic lipid was found to be the species of the membrane that increased the MgdA activity 7-fold whereas two other lipids (PG and PE) had only minor effects on MgdA. Additionally, a working model of MgdA for the biosynthesis and flow of sugar lipids between Synechocystis membranes was proposed.The last model system was another integral membrane protein with a distinct structure but also a different function. The envelope stress sensor, CpxA and its interaction with E. coli membranes were studied. CpxA autophosphorylation activity was found to be positively regulated by phosphatidylethanolamine and negatively by anionic lipids. In contrast, phosphorylation of CpxR by CpxA revealed to be increased with PG but inhibited by CL. Non-bilayer lipids had a negative impact on CpxA phosphotransfer activity.Taken together, these studies provide a better understanding of the significance of the interplay of lipids and model membrane proteins discussed here.
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| 3. |
- Staal, Arie, et al.
(författare)
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Global terrestrial moisture recycling in Shared Socioeconomic Pathways
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The global water cycle has undergone considerable changes since pre-industrial times due to global climate change and land-use changes. These drivers will almost certainly continue to change during the course of this century. However, where, how, and to which extent terrestrial moisture recycling will change as a result remains unclear.Mutually consistent scenarios of climate change and land-use changes for the 21st century are provided by the Shared Socioeconomic Pathways (SSPs). The SSPs provide a framework of five different narratives involving varying degrees of challenges associated with mitigation or adaptation. From each narrative follow different implications for emissions, energy, and land use. The SSPs serve as the conceptual framework behind the sixth generation of the Coupled Model Intercomparison Project, CMIP6.Terrestrial moisture recycling is often assessed using atmospheric moisture tracking models. An example is UTrack, a Lagrangian model to track moisture through three-dimensional space. Here we present a new forward-tracking version of UTrack that is forced by output of a CMIP6 model to study how terrestrial moisture recycling may change across the globe until the end of the 21st century in a range of SSPs, from mild to severe: SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5. For this forcing, we chose the Norwegian Earth System Model version 2, or NorESM2. It has a temporal resolution of one day and a spatial resolution of 1.25° × 0.9375° at eight pressure levels.We find that across the 21st century, the global terrestrial moisture recycling ratio decreases with the severity of the Shared Socioeconomic Pathways (SSPs). We calculate a decrease in global terrestrial precipitation recycling by 2.1% with every degree of global warming. Because the SSPs represent internally consistent scenarios of both global warming and global land cover changes, it is hard to distinguish the relative contributions of these two, but the evidence points at a major influence of global warming on moisture recycling.We find spatial differences in trends in recycling ratios, but which are broadly consistent among SSPs. If a change in precipitation (either drying or wetting) coincides with an increase in terrestrial precipitation recycling ratio, we call it land-dominated. We call the change in precipitation ocean-dominated if it coincides with a decrease in terrestrial precipitation recycling ratio. Land dominance tends to occur in regions with already large terrestrial precipitation recycling ratios, mainly interior South America (land-dominated drying) and eastern Asia (land-dominated wetting). Land-dominated drying may also happen in eastern Europe, in central America and in subtropical sub-Saharan Africa. Ocean-dominance, mainly in the form of wetting, is found primarily in the high northern latitudes and in central Africa.We also simulated the changes in basin recycling for the 27 major river basins of the world, confirming the overall tendency of decreasing recycling with severity of the SSP, as well as its spatial variations.
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| 4. |
- Barrientos, Natalia, 1985-
(författare)
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Arctic Ocean benthic foraminifera preservation and Mg/Ca ratios : Implications for bottom water palaeothermometry
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Reconstructions of Arctic Ocean palaeotemperatures are needed to disentangle natural variability from anthropogenic changes and understand the role of ocean heat transport in forcing or providing feedbacks on Arctic climate change. Despite known complications with calcareous microfossil preservation in Arctic Ocean sediments, calcareous benthic foraminifera can be common in interglacial sequences. However, thus far they have been underutilized in palaeoceanographic studies. This thesis explores the application of the Mg/Ca palaeothermometry proxy for reconstructing bottom water temperatures (BWT) in the Arctic Ocean during the late Quaternary. This method, which is supported by previous empirical studies demonstrating a strong temperature control on trace Mg inclusion into foraminiferal shell calcite, has been applied in many ocean regions and time intervals. Until now its application in the Arctic Ocean has been sparingly explored.The results of this doctoral thesis are based on benthic foraminifera retrieved from marine sediment cores covering a wide geographical Arctic Ocean area including both the shallow and vast continental shelves and slopes to the intermediate-to-deep waters of the Lomonosov Ridge and Morris Jesup Rise. These provide the first benthic foraminifera Mg/Ca ratios from the central Arctic Ocean region. In the first study, mechanisms that could affect Mg incorporation in Arctic benthic foraminifera are investigated using oceanographic field data and six 'live' modern Arctic species (Elphidium clavatum, Nonionella labradorica, Cassidulina neoteretis, Oridorsalis tener, Cibicidoides wuellerstorfi and Quinqueloculina arctica). The result is new species-specific Mg/Ca–BWT field calibrations that provide important constraints at the cold end of the BWT spectrum (-2 to 1°C) (Paper I). Using the new Mg/Ca–BWT equation for E. clavatum, a palaeotemperature record was generated for the late Holocene (past ca. 4100 yr) from the western Chukchi Sea. The data showed BWT fluctuations from -2 to 1°C that are interpreted as showing pulses of warmer Pacific water inflow at 500–1000 yr periods, thus revealing multi-centennial variability in heat transport into the Arctic Ocean driven by low latitude forcings (Paper II). Complications with foraminiferal calcite preservation that limit Mg/Ca palaeothermometry in the Arctic were discovered and these are tackled in two additional papers. Anomalously high Mg content in benthic foraminifera from the central Arctic Ocean is linked to diagenetic contamination as a result of the unique oceanographic, sedimentary and geochemical environment (Paper III). Lastly, the dramatic post-recovery dissolution of foraminifera from a Chukchi Shelf sediment core during core storage is investigated and attributed to acidification driven by sulphide oxidation in this organic rich and calcite poor shelf setting (Paper IV).The findings of this thesis demonstrate that benthic foraminiferal Mg/Ca-palaeothermometry can be applied in the Arctic Ocean and capture small BWT change (on the order of -2 to 2°C) even at low temperatures. In practice, preservational complexities can be limiting and require special sample handling or analysis due to the high potential for diagenetic contamination in the central Arctic Ocean and rapid post coring calcite dissolution in the seasonally productive shelf seas. This Ph.D. project is a component of the multidisciplinary SWERUS-C3 (Swedish-Russian-US Arctic Ocean Climate-Cryosphere- Carbon Interactions) project that included an expedition with Swedish icebreaker Oden to the East Siberian Arctic Ocean.
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| 5. |
- Hildebrandt, Franziska, 1994-
(författare)
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Host-parasite interactions in space and time
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Unicellular parasites of the apicomplexan phylum have a considerable effect on global health and agriculture. Two prominent examples of this phylum include malaria causing parasites of the Plasmodium genus and the widely prevalent parasite Toxoplasma gondii. While sharing a common ancestor, these parasites occupy unique biological niches, follow distinct life cycles, and result in different courses and outcomes of disease. In response to the parasite, the mammalian host has developed efficient and effective defense strategies. However, both Plasmodium and Toxoplasma have evolved strategies to evade the host’s defense response. Plasmodium parasites infect distinct tissues and cell types whereas T. gondii parasites are highly promiscuous and infect all nucleated cells. The identification of key factors involved in the interaction between the host and parasite is crucial for disease intervention, prevention, and eventually eradication efforts.Next-generation sequencing technologies have proven effective tools to investigate the response in a tissue or cell population of an infected organism. Novel genomics methods such as single-cell RNA-seq and spatial transcriptomics have enabled the investigation of heterogeneous transcriptional responses of individual cells in a population as well as heterogeneous expression profiles at spatially distinct tissue positions across entire tissue sections. This thesis pioneers the exploration of these methods in discerning the enormous complexity underlying host-parasite interplay.In Paper I, we determine spatial components of naive mouse liver in its true tissue context. We define gene expression gradients of pericentral and periportal zones in the liver and predict vein types with ambiguous annotations, based on in situ transcriptional profiles. We further identify novel spatial structures with distinct transcriptional profiles, associated with tissue integrity and integrate cell type proportions across the tissue.In Paper II we investigate host-pathogen interactions in P. berghei infected liver sections with spatiotemporal resolution. We establish spatial gene expression gradients from infection sites exhibiting upregulation of lipid metabolism associated genes 38 hours post-infection, suggesting a potential role of these pathways in immune evasion. We further show that local and systemic inflammation are delayed but not ablated in salivary gland lysate challenged control livers and propose that local inflammatory hotspots may represent an important spatial component for parasite development in the liver.In Paper III we use dual scRNA-seq to investigate heterogeneous transcription of mouse bone marrow-derived dendritic cells (BMDCs) infected with two distinct genotypes of T. gondii parasites. We show differential responses towards the two T. gondii genotypes in two distinct subpopulations of BMDCs over multiple time points post infection. Moreover, we generate co-expression networks that define host and parasite genes, which are likely involved in the modulation of host immunity.In summary, this thesis aims to characterize host-pathogen interactions of two major apicomplexan genera in two distinct cell niches of the murine host with spatiotemporal or single cell resolution. In detail, this encompasses the study of spatial structures of the host in the liver environment and the spatiotemporal consequences of an infection with P. berghei. Furthermore, the aims include deciphering heterogeneous interactions between two distinct T. gondii strains and infected BMDCs.
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| 6. |
- Samuelsson, Göran S., et al.
(författare)
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Large-scale field study on thin-layer capping of dioxin contaminated sediments in the Grenland fjords, Norway : Effects on marine benthic fauna
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The Grenland fjords on the South East Coast of Norway are heavily contaminated with dioxins and furans after emissions from past industrial activities. Thin layer capping with a 1.1 to 3.7 cm cap was tested as a remediation option in a large-scale in situ study in two different parts of the fjord system, in the Ormefjord at 25-30 meters depth and in the Eidangerfjord at 80-100 meters depth. Three different capping materials: Limestone gravel, Clay, and powdered activated carbon (AC) mixed into clay (AC+clay) was compared to untreated reference fields in order to evaluate their effects on contaminant sequestering and possible effects on the benthic communities. Sediment to water fluxes of contaminants were significantly reduced by the capping materials, especially with AC-clay and is reported in a companion study.This study discusses the ecological effects of the remediation 1 and 14 months post treatment. Capping with Clay and Lime had minor and short-lasting effects on benthic fauna. Capping with AC+clay, however, had led to profound and more long-lasting perturbations of the macrofauna. An initial massive decline in filter feeders and suspension feeders was observed after 1 month in the shallower Ormefjord. The negative effects got worse after 14 months and resulted in dramatic reductions of all feeding guilds. The number of species, organism abundances and biomass in the AC+clay field were ca 80-90 % lower compared to the reference fields after 14 months.The negative effects were less pronounced at the deeper (80-100 meters) location in the Eidangerfjord and were also stable with time, suggesting that the benthic community the deeper habitat was more resilient to the capping compared to the shallower community in Ormefjord.The differences in response of the two communities are hypothesized to be due to the higher macrofaunal diversity in the deeper location, as well as to differences in abiotic factors such as available food and temperature. Results from this study show that amendment with powdered AC can lead to serious perturbations of the benthic community, at least initially, i.e. one year post capping in this study. These results stresses that further long-term monitoring of these benthic communities is necessary before capping with AC+clay could be advocated as a potential remediation option.
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| 7. |
- Samuelsson, Göran S., et al.
(författare)
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Reduced bioaccumulation of PCBs and PAHs by sediment fauna following in situ remediation with activated carbon in Trondheim Harbor (Norway)
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Thin-layer capping with activated carbon (AC) was deployed in experimental plots in Trondheim harbor, Norway, using caps containing AC+clay, AC-only or AC+sand. Intact sediment cores were collected from the in situ remediated plots to study the capping efficiency of the various AC treatments in reducing the aqueous concentrations and the bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) in the polychaete Hediste diversicolor and the clam Abra nitida. Reduced aqueous concentrations were observed in all AC-treatments, but generally AC+clay appeared to be superior to the other tested treatments. Capping efficiency by AC+clay, in terms of reduced bioaccumulation of PAHs and PCBs, ranged between 40 % and 87% in the worms and between 67% and 97% in the clams. Sediment capped with AC-only also led to reduced bioaccumulation of PCBs, while AC+sand showed no reduction in bioaccumulation. The worms had lower relative lipid content in the AC-only treatment after exposure.
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| 8. |
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| 9. |
- Höglander, Helena, et al.
(författare)
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Pelagial biologi - växtplankton
- 2012
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Ingår i: Havet. - Stockholm : Naturvårdsverket. - 9789187025129 - 9789198064612 ; , s. 48-49
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 10. |
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