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Soil organic matter (SOM) contains about twice the amount of carbon in the atmosphere. With global changes, the potential shifts in SOM quantity and quality are a major concern. Due to its heterogeneity, SOM remains largely unknown in terms of its molecular composition and responses to climatic events. Traditional bulk soil analysis cannot depict the structural changes in SOM. This thesis applies two complementary molecular-level methods, i.e., SOM biomarker gas chromatography/mass spectrometry (GC/MS) and nuclear magnetic resonance (NMR) spectroscopy, to examine the origin and degradation of various SOM components in grassland and temperate forest soils, and to investigate the shifts in microbial community and SOM composition with both laboratory- and field-simulated global changes, such as frequent freeze-thaw cycles, increasing soil temperatures, elevated atmospheric CO2 levels, and nitrogen (N) deposition. This thesis has several major findings. First, as the most active component in soil, microbial communities were sensitive to substrate availability changes resulting from prolonged soil incubation, freeze-thaw-induced cell lyses, N fertilization and increased plant inputs under elevated CO2 or soil warming. Microbial community shifts have direct impacts on SOM decomposition patterns. For instance, an increased fungal community was believed to contribute to the enhanced lignin oxidation in an in situ soil warming experiment as the primary degrader of lignin in terrestrial environments. Second, contrast to the conventional belief that aromatic structure was recalcitrant and stable in SOM, ester-bond aliphatic lipids primarily originating from plant cutin and suberin were preferentially preserved in the Canadian Prairie grassland soil profiles as compared with lignin-derived phenols. Cutin- and suberin-derived compounds also demonstrated higher stability during soil incubation. With an increased litter production under elevated CO2 or global warming, an enrichment of alkyl structures that had strong contributions from leaf cuticles was observed in the Duke Forest Free Air CO2 Enrichment (FACE) and soil warming experiments, suggesting an accumulation of plant-derived recalcitrant carbon in the soil. These results have significant implications for carbon sequestration and terrestrial biogeochemistry. Overall, this thesis represents the first of its kind to employ comprehensive molecular-level techniques in the investigation of SOM structural alterations under global changes.

Soil organic matter (SOM) contains about twice the amount of carbon in the atmosphere. With global changes, the potential shifts in SOM quantity and quality are a major concern. Due to its heterogeneity, SOM remains largely unknown in terms of its molecular composition and responses to climatic events. Traditional bulk soil analysis cannot depict the structural changes in SOM. This thesis applies two complementary molecular-level methods, i.e., SOM biomarker gas chromatography/mass spectrometry (GC/MS) and nuclear magnetic resonance (NMR) spectroscopy, to examine the origin and degradation of various SOM components in grassland and temperate forest soils, and to investigate the shifts in microbial community and SOM composition with both laboratory- and field-simulated global changes, such as frequent freeze-thaw cycles, increasing soil temperatures, elevated atmospheric CO2 levels, and nitrogen (N) deposition. This thesis has several major findings. First, as the most active component in soil, microbial communities were sensitive to substrate availability changes resulting from prolonged soil incubation, freeze-thaw-induced cell lyses, N fertilization and increased plant inputs under elevated CO2 or soil warming. Microbial community shifts have direct impacts on SOM decomposition patterns. For instance, an increased fungal community was believed to contribute to the enhanced lignin oxidation in an in situ soil warming experiment as the primary degrader of lignin in terrestrial environments. Second, contrast to the conventional belief that aromatic structure was recalcitrant and stable in SOM, ester-bond aliphatic lipids primarily originating from plant cutin and suberin were preferentially preserved in the Canadian Prairie grassland soil profiles as compared with lignin-derived phenols. Cutin- and suberin-derived compounds also demonstrated higher stability during soil incubation. With an increased litter production under elevated CO2 or global warming, an enrichment of alkyl structures that had strong contributions from leaf cuticles was observed in the Duke Forest Free Air CO2 Enrichment (FACE) and soil warming experiments, suggesting an accumulation of plant-derived recalcitrant carbon in the soil. These results have significant implications for carbon sequestration and terrestrial biogeochemistry. Overall, this thesis represents the first of its kind to employ comprehensive molecular-level techniques in the investigation of SOM structural alterations under global changes.

Global environmental changes, especially land-use changes, have profound effects on both ecosystem functioning and biodiversity, having already altered many ecosystem services. These losses emphasize the need to preserve what remains; however when conservation programs are not sufficient, restoring areas that have been destroyed or disturbed can improve conservation efforts and mitigate damages. This work focuses on campos rupestres, Neotropical grasslands found at altitudes, which are part of the Cerrado (Brazilian savannas). They host a great biodiversity with a high level of endemism and, like other mountain ecosystems, provide valuable ecosystem services, such as water purification and recreational services. They have been and still are being impacted by human activities, such as civil engineering construction, quarrying or mining. The first objective of this thesis was to describe the reference ecosystem in order to aim for a clear restoration target and to monitor progress and success. We show that campos rupestres are composed of at least two distinct plant communities (i.e. sandy and stony grasslands), each having a specific composition and structure, hosting a great biodiversity. Several phenological patterns occur among the herbaceous communities: the majority of species flowers and fruits appear during the rainy season but other patterns can be observed. During our 2-year survey, some dominant species belonging to Poaceae, among others, were not observed reproducing, which implies limited chances to disperse on degraded areas. Campo rupestre vegetation is not resilient following a strong disturbance: several years after the disturbance, almost no native species are encountered on the degraded areas, soils are completely altered and seed bank recomposes only with non-target ruderal species. According to the filter model, a local community is a subset of the regional species pool determined by a set of dispersal, abiotic and biotic filters. Acting on the different filters to influence the plant community was the core of our restoration interventions. We then applied three in-situ restoration protocols (hay transfer, species translocation and turf translocation) to restore both kinds of grassland. Hay transfer does not allow the restoration of campo rupestre vegetation because of soil alteration and mainly because of poor seed quality. Indeed, germination studies show that, while some Xyridaceae and Velloziaceae have a high germinability, some dominant Poaceae, Cyperaceae or Asteraceae species have embryoless, unviable or dormant seeds, which makes seeding less efficient. There is no evidence that fire-related cues enhance germination in campos rupestres. Species translocation is successful for only one species, Paspalum erianthum; for the others, root damages probably impede survival. Finally, turf translocation is the most successful method, since numerous species are re-introduced on degraded areas. However due to the low resilience of pristine campos rupestres where turfs are taken from, turf translocation can only be considered in the case of habitat rescue, in circumstances when complete habitat destruction is otherwise unavoidable. Face to the difficulty to restore these peculiar grasslands, the protection and the conservation of campos rupestres must be made a high priority