| 1. |
- Andersson, Erika, et al.
(author)
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A contrast variation SANS and SAXS study of soil derived dissolved organic matter, and its interactions with hematite nanoparticles
- 2023
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In: JCIS Open. ; 11
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Journal article (peer-reviewed)abstract
- Soil derived dissolved organic matter (DOM) is an important component of the carbon cycle and influences numerous biogeochemical processes, including the formation of mineral-organic associations. DOM ranges in size from small organic molecules to macromolecules and colloidal aggregates. In this study we have used small angle neutron (SANS) and X-ray (SAXS) scattering to characterize the colloidal DOM fraction from the organic layer of a boreal forest soil, and its interactions with hematite (α-Fe2O3) mineral nanoparticles. Comparison between SAXS and contrast variation SANS patterns revealed that the scattering form factor of the colloidal DOM aggregates was essentially independent of the scattering contrast, implying that the colloidal aggregates have an essentially homogeneous chemical composition, down to the nanometre length scale. Variation of the D2O/H2O ratio of the solvent yielded a SANS intensity minimum at ca. 40 vol % D2O, which was consistent with colloids composed of mainly polysaccharides. At pH 5.5 the pure hematite nanoparticles were colloidally stable in water and characterized by a ζ-potential of +25 mV and a hydrodynamic radius of ca. 70 nm. In the presence of DOM, the hematite nanoparticles lost the colloidal stability and aggregated into larger clusters, displaying a negative ζ-potential of ca. −25 mV. The charge reversal suggested that negatively charged polyanions of DOM adsorbed onto the hematite particles, possibly leading to bridging flocculation. Our results suggested that mainly low molecular weight components induced hematite aggregation because no or very limited interactions between DOM colloids and hematite were detected.
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| 2. |
- Andersson, Erika, et al.
(author)
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Generation and properties of organic colloids extracted by water from the organic horizon of a boreal forest soil
- 2023
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In: Geoderma. - : Elsevier BV. - 0016-7061. ; 432
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Journal article (peer-reviewed)abstract
- Organic colloids are an important part of dissolved organic matter (DOM) yet many of their properties remain elusive. The main aims of this study were to assess how the colloidal properties of DOM extracted with water from an organic boreal soil horizon varied with the extraction protocol, and thereby provide insight into the nature of the DOM colloids and develop a mechanistic understanding of how the colloids were generated from the parent soil aggregates. This was accomplished by systematic variations of extraction temperature (4 °C–100 °C), time, mechanical agitation, and pH, together with a combination of chemical analyses, and light and X-ray scattering. Our results agreed with the previous identification of two main colloidal DOM species, one fractal cluster and a second, smaller colloidal DOM species described as chains or coils. Fractal clusters completely dominated the colloidal DOM in extracts from our soil at room temperature and below. Colloidal coils only existed in DOM extracted above room temperature, and their amount increased significantly between 50 °C–100 °C. Moreover, the temperature variation indicated that the fractal clusters partly dissolved into colloidal coils at elevated temperatures. Mechanical agitation at 4 °C significantly increased the amount of DOM extracted, increasing the concentrations of both fractal clusters and low-molecular weight organic compounds. While the clusters were extracted from agitated and non-agitated soil suspensions, the low molecular weight organics were mainly released by agitation. Based on the experimental observations, we propose a conceptual model where parent soil aggregates contain the fractal clusters in mobile and occluded forms, and that the occluded clusters co-exist with occluded low molecular weight organics. These occluded forms may be released by mechanical forces, increasing pH and temperature. At higher temperatures, the soil aggregates and the fractal clusters start to break up, and subsequently individual colloidal coils, presumably carbohydrates, disperse in the water phase. The model explains the origin and properties of the fractal clusters that completely dominate the colloidal DOM extracted from our soil at room temperature and below.
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| 3. |
- Koder Hamid, Mona, et al.
(author)
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Molecular dynamics simulations of the adsorption of an intrinsically disordered protein: Force field and water model evaluation in comparison with experiments
- 2022
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In: Frontiers in Molecular Biosciences. - : Frontiers Media SA. - 2296-889X. ; 9
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Journal article (peer-reviewed)abstract
- This study investigates possible structural changes of an intrinsically disordered protein (IDP) when it adsorbs to a solid surface. Experiments on IDPs primarily result in ensemble averages due to their high dynamics. Therefore, molecular dynamics (MD) simulations are crucial for obtaining more detailed information on the atomistic and molecular levels. An evaluation of seven different force field and water model combinations have been applied: (A) CHARMM36IDPSFF + CHARMM-modified TIP3P, (B) CHARMM36IDPSFF + TIP4P-D, (C) CHARMM36m + CHARMM-modified TIP3P, (D) AMBER99SB-ILDN + TIP3P, (E) AMBER99SB-ILDN + TIP4P-D, (F) AMBERff03ws + TIP4P/2005, and (G) AMBER99SB-disp + disp-water. The results have been qualitatively compared with those of small-angle X-ray scattering, synchrotron radiation circular dichroism spectroscopy, and attenuated total reflectance Fourier transform infrared spectroscopy. The model IDP corresponds to the first 33 amino acids of the N-terminal of the magnesium transporter A (MgtA) and is denoted as KEIF. With a net charge of +3, KEIF is found to adsorb to the anionic synthetic clay mineral Laponite® due to the increase in entropy from the concomitant release of counterions from the surface. The experimental results show that the peptide is largely disordered with a random coil conformation, whereas the helical content (α- and/or 310-helices) increased upon adsorption. MD simulations corroborate these findings and further reveal an increase in polyproline II helices and an extension of the peptide conformation in the adsorbed state. In addition, the simulations provided atomistic resolution of the adsorbed ensemble of structures, where the arginine residues had a high propensity to form hydrogen bonds with the surface. Simulations B, E, and G showed significantly better agreement with experiments than the other simulations. Particularly noteworthy is the discovery that B and E with TIP4P-D water had superior performance to their corresponding simulations A and D with TIP3P-type water. Thus, this study shows the importance of the water model when simulating IDPs and has also provided an insight into the structural changes of surface-active IDPs induced by adsorption, which may play an important role in their function.
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| 4. |
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| 5. |
- Krumina, Lelde, et al.
(author)
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Ectomycorrhizal Fungal Transformation of Dissolved Organic Matter : Consequences for Reductive Iron Oxide Dissolution and Fenton-Based Oxidation of Mineral-Associated Organic Matter
- 2022
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In: Frontiers in Earth Science. - : Frontiers Media SA. - 2296-6463. ; 10
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Journal article (peer-reviewed)abstract
- Recent studies have shown that dissolved organic matter (DOM) decomposed by ectomycorrhizal (ECM) fungi increases adsorptive properties of organic matter towards soil mineral surfaces. Concomitantly, ECM fungi secrete secondary metabolites with iron reducing capacity that are thought to participate in non-enzymatic Fenton-based decomposition of DOM. The aim of this study was to investigate if the iron reduction induced by the ECM fungus Paxillus involutus during organic matter decomposition was conserved in the decomposed DOM. We explored how the modified DOM reductively dissolved ferrihydrite and goethite nanoparticles and how these processes affected the reactions with H2O2 and the Fenton-based oxidation of mineral-associated organic matter. Culture filtrates were obtained from incubation of the ECM fungus on DOM from forest litter of a spruce forest. This modified DOM was separated by extraction into an ethyl acetate and a water fraction. These fractions were reacted with ferrihydrite and goethite in absence and presence of H2O2. Dissolved Fe2+ and HO• were measured and the reactions at the iron oxide-water interfaces were monitored in real-time with in-situ IR spectroscopy. Experiments showed that decomposition of DOM by P. involutus generated a modified DOM that displayed an increased and persistent reductive capacity. Most of the reductants were isolated in the aromatic- and carboxyl-dominated ethyl acetate fraction but some reduction capacity was also captured in the water fraction mainly containing carbohydrates. Reductive dissolution was more extensive for ferrihydrite than goethite, and this process generated significant oxidation of the DOM-ferrihydrite associations. Oxidation of adsorbed DOM was triggered by H2O2 via heterogenous and homogeneous Fenton reactions. These oxidation processes were favored by ferrihydrite because of a high reduction potential and a high efficiency of heterogeneous Fenton as compared to goethite. An optimal timing between the heterogeneous and homogeneous Fenton processes triggered extensive radical oxidation of the DOM-ferrihydrite associations generating a high concentration of surface-associated oxalate. Overall, the results show that organic matter associated with ferrihydrite may be more susceptible to radical oxidation than on goethite, and that fungal decomposition of DOM in general may have consequences for other important soil processes such as mineral dissolution, adsorption and initiation of radical reactions.
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| 6. |
- Mafla-Endara, Paola M, et al.
(author)
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Exposure to polystyrene nanoplastics reduces bacterial and fungal biomass in microfabricated soil models
- 2023
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In: Science of the Total Environment. - 1879-1026. ; 904
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Journal article (peer-reviewed)abstract
- Nanoplastics have been proven to induce toxicity in diverse organisms, yet their effect on soil microbes like bacteria and fungi remains largely unexplored. In this paper, we used micro-engineered soil models to investigate the effect of polystyrene (PS) nanospheres on Pseudomonas putida and Coprinopsis cinerea. Specifically, we explored the effects of increasing concentrations of 60 nm carboxylated bovine serum albumin (BSA) coated nanospheres (0, 0.5, 2, and 10 mg/L) on these bacterial and fungal model organisms respectively, over time. We found that both microorganisms could disperse through the PS solution, but long-distance dispersal was reduced by high concentrations. Microbial biomass decreased in all treatments, in which bacteria showed a linear dose response with the strongest effect at 10 mg/L concentration, and fungi showed a non-linear response with the strongest effect at 2 mg/L concentration. At the highest nanoplastics concentration, the first colonizing fungal hyphae adsorbed most of the PS nanospheres present in their vicinity, in a process that we termed the 'vacuum cleaner effect'. As a result, the toxicity effect of the original treatment on subsequently growing fungal hyphae was reduced to a growth level indistinguishable from the control. We did not find evidence that nanoplastics are able to penetrate bacterial nor fungal cell walls. Overall, our findings provide evidence that nanoplastics can cause a direct negative effect on soil microbes and highlight the need for further studies that can explain how the microbial stress response might affect soil functions.
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| 7. |
- Meklesh, Viktoriia, et al.
(author)
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Characterization of the Colloidal Properties of Dissolved Organic Matter From Forest Soils
- 2022
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In: Frontiers in Soil Science. - : Frontiers Media SA. - 2673-8619.
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Journal article (peer-reviewed)abstract
- Components of dissolved organic matter (DOM) span from sub-nm molecules to colloidal aggregates of several hundred nm. The colloidal fraction is important for the transport of organic matter and associated elements in the environment, and for the stability of DOM constituents with respect to microbial decomposition. This study focuses on the colloidal properties of DOM extracted from spruce forest soils of a chronosequence. The DOM samples were obtained by common water extraction procedures at 21 and 100°C, respectively. We applied an experimental approach combining chemical analysis with light and X-ray scattering techniques that informed on the colloidal size, charge, and structure of DOM. Results showed that two main types of colloids were present: semi-flexible cylinders and fractal aggregates. The cylinders consisted of carbohydrates, presumably hemicelluloses, while the aggregates were a composite material containing a large fraction of carbohydrates together with aliphatics and clay particles. These fractal aggregates dominated the cold-water extracts whereas the strong increase in total organic carbon by hot-water extraction caused a concomitantly strong increase of semi-flexible cylinders, which became the predominant species. Comparison between the chronosequence soils showed that with increasing forest age, the amount of carbon extracted per gram of soil declined and the concentration of the semi-flexible cylinders decreased. Thus, the distribution between the fractal aggregates and cylinders in the forest soil DOM samples depends on the composition of the soil organic matter and the leaching temperature. Changes in this distribution may have important implications for the reactivity and stability of DOM colloids.
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