Environmental pollution of heavy metals has become an increasing problem. Environmental risk assessments can be conducted to investigate and determine the potential risk of polluted terrestrial environments. Traditionally, risk assessments are based on total soil metal concentrations on a dry weight basis. Assessments based on total concentrations do not account for metal bioavailability. The bioavailable fraction of the metal is that available for metabolic uptake over a biological membrane, and it is largely controlled by the physiochemical characteristics of the soil solution. For soil-dwelling organisms the most important physiochemical parameters governing copper toxicity are pH and dissolved organic carbon. To incorporate these parameters into risk assessments mechanistic chemical equilibrium models can be used, such as biotic ligand models. These have previously been applied to mainly aquatic environments and only in recent years they have been expanded to the terrestrial realm. The overall aim of this thesis was to test the applicability of a leachate-based biotic ligand model, which takes pH dependency into account, for ecotoxicological risk assessment of soil-dwelling organisms. Toxicity data with associated soil solution pH for seven soil-dwelling organisms and microbially mediated soil processes were obtained from the Swedish Geotechnical Institute. Physiochemical soil characteristics of three Swedish field sampled soils amended with biochar were also obtained from the Swedish Geotechnical Institute. The toxicity data were used to derive two key parameters for calibration of the soil biotic ligand model through linear regression analysis i.e., the pH dependency and the species-specific intrinsic sensitivity. The calibrated biotic ligand models were applied to the field soils and species sensitivity distributions were derived for each soil to calculate hazardous metal concentrations. A simplified risk assessment of the soils was performed based on the results of the leachate-based biotic ligand models and on measured total concentrations on a dry weight basis.  As expected, the results of the regression analysis showed a strong pH dependency between toxicity effect concentrations and pH. For all included test organisms, the copper toxicity effect concentration decreased as the pH of the soil solution increased. Although Cu2+ toxicity increased with increasing pH, the considered organisms showed individual and varying pH-dependencies especially at pH 3-4 and pH 7-8. Further, the results showed that the risk assessment based on the Swedish EPA method, which use total metal concentrations on a dry weight basis, yielded different results than risk assessment based on the leachate-based biotic ligand models. The soils that had been amended with biochar contained lower total Cu concentrations on a dry weight basis compared to those which had not been amended. Consequently, total Cu concentrations exceeded the guideline value for sensitive land-use only in the non-amended soils. Total Cu concentrations exceeded the guideline value for less sensitive land-use in all field soils. Similar to total Cu concentrations on a dry weight basis, the total dissolved Cu concentrations also decreased with added biochar. The same trend could not be seen for Cu2+ in CaCl2 leachates. DOC in the leachates decreased with added biochar, suggesting that biochar sorbs DOC. A majority of the total dissolved Cu was bound to DOC and only a small fraction left as free ions.  The lower DOC concentrations led to higher Cu2+ concentrations in the leachate. Consequently, two of the biochar amended soils had Cu2+ concentrations exceeding the calculated HC50 (protection level for LSL). The predicted toxic effect concentrations ranged from 0.001 μg/L for the most sensitive organism Tomato shoot (L. esculentum) to 3.53 μg/L for the least sensitive organism Soil induced respiration (SIR). The most sensitive field soil had the highest measured pH and had been amended with 6% biochar, the two least sensitive field soils had the lowest measured pH and had been amended with 3 and 6% biochar respectively. The risk assessment based on the soil-BLM approach yielded different, but not less conservative, results compared to the traditional risk assessment based on total concentrations on a dry weight basis. The expected result was for the BLM-based risk assessment to be less conservative as it takes the site-specific bioavailability into account. The leachate-based soil-BLM seems to be sensitive to changes and variations of the input parameters in the speciation. To improve the robustness of the model, and accuracy of risk assessments, additional organisms should be included in the SSDs and speciation should be performed on soils with a wider range of pH. The potential of leachate-based BLMs for risk assessment has been demonstrated. The results invite to further v development of leachate-based soil-BLMs and has the potential to increase the knowledge of the chemistry and toxicology of copper in soils as well as the effects and behaviour of biochar as a metal sorbent.

Nitrogen (N), an essential plant macronutrient, is among the most limiting factors of crop yield. To sustain modern agriculture, N is often amended in soil in the form of chemical N fertilizer, a major anthropogenic contributor to nutrient pollution that affects climate, biodiversity and human health. To achieve agricultural sustainability, a comprehensive understanding of the regulation of N response in plants is required, in order to engineer crops with higher N use efficiency. Recently, epigenetic mechanisms, such as histone modifications, have gained increasing importance as a new layer of regulation of biological processes. However, our understanding of how epigenetic processes regulate N uptake and assimilation is still in its infancy. To fill this knowledge gap, we first performed a meta-analysis that combined functional genomics and network inference approaches to identify a set of N-responsive epigenetic regulators and predict their effects in regulating epigenome and transcriptome during plant N response. Our analysis suggested that histone modifications could serve as a regulatory mechanism underlying the global transcriptomic reprogramming during plant N response. To test this hypothesis, I applied chromatin immunoprecipitation-sequencing (ChIP-Seq) to monitor the genome-wide changes of four histone marks (H3K27ac, H3K4me3, H3K36me3 and H3K27me3) in response to N supply in tomato plants, followed by RNA-Seq to profile the transcriptomic changes. To investigate the organ specificity of histone modifications, I assayed shoots and roots separately. My results suggest that up to two-thirds of differentially expressed genes (DEGs) are modified in at least one of the four histone marks, supporting an integral role of histone modification in regulating N response. I observed a synergistic modification of active histone marks (H3K27ac, H3K4me3 and H3K36me3) at gene loci functionally relevant to N uptake and assimilation. Surprisingly, I uncovered a non-canonical role of H3K27me3, which is conventionally associated with repressed genes, in modulating active gene expression. Interestingly, such regulatory role of H3K27me3 is specifically associated with highly expressed genes or low expressed genes, depending on the organ context. Overall, I revealed the multi-faceted role of histone marks in mediating the plant N response, which will guide breeding and engineering of better crops with higher N use efficiency