Soil microbiology has entered into the big data era, but the challenges in bridging laboratory\uffe2\uff80\uff90, field\uffe2\uff80\uff90, and model\uffe2\uff80\uff90based studies of ecosystem functions still remain. Indeed, the limitation of factors in laboratory experiments disregards interactions of a broad range of in situ environmental drivers leading to frequent contradictions between laboratory\uffe2\uff80\uff90 and field\uffe2\uff80\uff90based studies, which may consequently mislead model development and projections. Upscaling soil microbiology research from laboratory to ecosystems represents one of the grand challenges facing environmental scientists, but with great potential to inform policymakers toward climate\uffe2\uff80\uff90smart and resource\uffe2\uff80\uff90efficient ecosystems. The upscaling is not only a scale problem, but also requires disentangling functional relationships and processes on each level. We point to three potential reasons for the gaps between laboratory\uffe2\uff80\uff90 and field\uffe2\uff80\uff90based studies (i.e., spatiotemporal dynamics, sampling disturbances, and plant\uffe2\uff80\uff93soil\uffe2\uff80\uff93microbial feedbacks), and three key issues of caution when bridging observations and model predictions (i.e., across\uffe2\uff80\uff90scale effect, complex\uffe2\uff80\uff90process coupling, and multi\uffe2\uff80\uff90factor regulation). Field\uffe2\uff80\uff90based studies only cover a limited range of environmental variation that must be supplemented by laboratory and mesocosm manipulative studies when revealing the underlying mechanisms. The knowledge gaps in upscaling soil microbiology from laboratory to ecosystems should motivate interdisciplinary collaboration across experimental, observational, theoretic, and modeling research.
", "keywords": ["2. Zero hunger", "0301 basic medicine", "field in situ observation", "0303 health sciences", "soil biogeochemistry", "microbial-based models", "Models", " Theoretical", "Plants", "15. Life on land", "soil microbiology", "Soil", "03 medical and health sciences", "laboratory incubation", "13. Climate action", "Perspective", "global change factors", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/gcb.16537"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/gcb.16537", "name": "item", "description": "10.1111/gcb.16537", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcb.16537"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-28T00:00:00Z"}}, {"id": "10.1111/j.1365-2486.2012.02749.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:18:50Z", "type": "Journal Article", "created": "2012-05-24", "title": "Experimental Litterfall Manipulation Drives Large And Rapid Changes In Soil Carbon Cycling In A Wet Tropical Forest", "description": "AbstractGlobal changes such as variations in plant net primary production are likely to drive shifts in leaf litterfall inputs to forest soils, but the effects of such changes on soil carbon (C) cycling and storage remain largely unknown, especially in C\uffe2\uff80\uff90rich tropical forest ecosystems. We initiated a leaf litterfall manipulation experiment in a tropical rain forest in Costa Rica to test the sensitivity of surface soil C pools and fluxes to different litter inputs. After only 2\uffc2\uffa0years of treatment, doubling litterfall inputs increased surface soil C concentrations by 31%, removing litter from the forest floor drove a 26% reduction over the same time period, and these changes in soil C concentrations were associated with variations in dissolved organic matter fluxes, fine root biomass, microbial biomass, soil moisture, and nutrient fluxes. However, the litter manipulations had only small effects on soil organic C (SOC) chemistry, suggesting that changes in C cycling, nutrient cycling, and microbial processes in response to litter manipulation reflect shifts in the quantity rather than quality of SOC. The manipulation also affected soil CO 2 fluxes; the relative decline in CO 2 production was greater in the litter removal plots (\uffe2\uff88\uff9222%) than the increase in the litter addition plots (+15%). Our analysis showed that variations in CO 2 fluxes were strongly correlated with microbial biomass pools, soil C and nitrogen (N) pools, soil inorganic P fluxes, dissolved organic C fluxes, and fine root biomass. Together, our data suggest that shifts in leaf litter inputs in response to localized human disturbances and global environmental change could have rapid and important consequences for belowground C storage and fluxes in tropical rain forests, and highlight differences between tropical and temperate ecosystems, where belowground C cycling responses to changes in litterfall are generally slower and more subtle.
", "keywords": ["2. Zero hunger", "soil biogeochemistry", "microbial biomass", "soil nitrogen", "carbon dioxide", "04 agricultural and veterinary sciences", "dissolved organic matter", "Biogeochemistry", "15. Life on land", "soil carbon chemistry", "root biomass", "13. Climate action", "soil phosphorus", "0401 agriculture", " forestry", " and fisheries", "net primary productivity"]}, "links": [{"href": "https://doi.org/10.1111/j.1365-2486.2012.02749.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1365-2486.2012.02749.x", "name": "item", "description": "10.1111/j.1365-2486.2012.02749.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1365-2486.2012.02749.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-06-25T00:00:00Z"}}, {"id": "10.3929/ethz-b-000648810", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:20:57Z", "type": "Journal Article", "title": "Transformation of jarosite and iron oxyhydroxides in acid sulfate paddy soils", "description": "Open AccessMinerals containing Fe are ubiquitous in soils. By providing an abundance of sites for the sorption and incorporation of major and trace elements, Fe minerals can govern the fate and behaviour of numerous pollutants and nutrients in soils. Furthermore, the reactivity of Fe in redox-dynamic soils produces a web of Fe mineral transformation processes with broad consequences for element cycling. The importance of Fe cycling is no exception in acid sulfate soils, although the high sulfur and low pH conditions produce unique Fe mineral transformation processes and compositions. In acid sulfate soils, jarosite, an Fe-K hydroxysulfate mineral, and ferrihydrite, a common short-range-ordered Fe oxyhydroxide mineral, play a central role in the pedological development of active and post-active acid sulfate soils. Soil pH and the dynamics of metals, such as aluminium, are key to understanding the toxicity of acid sulfate soils and can be directly influenced by jarosite and ferrihydrite transformation processes. Although the transformation of Fe minerals is a key component of biogeochemical processes in redox-active soils, the variables that control the rates and pathways of Fe mineral transformations in soil remain uncertain. The uncertainty arises from the difficulty of tracing molecular processes within a matrix of diverse soil components. Iron minerals are regularly characterised in soils, but the processes that explain the Fe mineral composition of soils cannot be easily resolved. An alternative approach is to perform simplified experiments, such as mixed mineral suspension experiments, under controlled laboratory conditions, to test the effect of individual variables. These systems often use synthetic minerals, although relatively pure jarosite may also be isolated from soils and tested in mixed suspension experiments. While useful to derive mechanistic understanding, the measured outcomes of mixed suspension experiments may not represent the rates and products of transformations that occur in soils. Therefore, the objective of this thesis was to gain new understanding of the stability and transformation of jarosite and ferrihydrite in acid sulfate soils by developing novel experimental techniques to follow the transformation of synthetic jarosite and ferrihydrite directly in soils. The central theme of the thesis is the comparison of jarosite and aluminium-substituted jarosite transformation in experimental media of increasing complexity. The experiments are performed under conditions that are relevant to rice paddy soils because of the importance of rice in global food production, and the unique management of rice paddies whereby regular flooding during the growing season produces distinct redox cycles. In Thailand, large areas of the Chao Phraya River delta are cultivated as rice paddies despite being acid sulfate soils, providing a suitable site to observe the effects of regular redox cycling on the biogeochemistry of Fe minerals in acid sulfate soils. The thesis begins with characterisation of synthetic and natural jarosite mineral composition and reactivity. Spectroscopic techniques (Raman spectroscopy, M\u00f6ssbauer spectroscopy and Energy-dispersive X-ray spectrometry) and X-ray diffraction (XRD) were used to assess the element substitution of mineral samples from two jarosite-alunite synthetic solid solution series. The same characterisation techniques were then applied to a sample of jarosite from an acid sulfate soil in Thailand has a natural Al-for-Fe substitution. The mineral characterisation was followed by a transformation experiment in a mixed-suspension system, similar to experimental designs that have been previously used to study mineral transformation processes. The experiment followed the transformation of the natural jarosite sample from an acid sulfate soil in Thailand and three jarosite samples with variable amounts of Al substitution. The reaction solution mimicked the pH (circumneutral) and Fe(II) content (up to 1:1 ratio of Fe(II) in solution to Fe(III) in solids) of flooded acid sulfate soils. Furthermore, using a 57Fe tracer, the simultaneous transformation processes that explained the distribution of mineral products could be resolved from one another. The transformation experiment revealed the relative reactivity of the minerals in the presence of Fe(II), and created a baseline that could be used to compare traditional mixed-suspension experiments with transformations in complex media such as soil. To advance mineral transformation experiments towards studies in which transformation processes may be followed within a soil matrix, several novel techniques were developed. In a first step, ferrihydrite was incubated for up to twelve weeks in microcosms, each containing 300 g of 5 mM CaCl2 solution and 250 g of one of five paddy soils. The ferrihydrite was buried in the soil within a mesh bag (polyethel terephthalate, 51 \u03bcm pores, 30 mm x 12 mm x 3 mm) that allowed free contact between the synthetic minerals and the pore water, but separated the minerals from direct contact with the soil matrix. The mineral products of the transformation were identified and quantified by Rietveld fitting of XRD patterns. Further, the spatial arrangements of the ferrihydrite and transformation products were measured after two weeks by Raman spectroscopy, which could be used to assess the effects of pore water chemistry and diffusion processes on mineral transformation in the mesh bags. The second step involved measuring jarosite and Al-substituted jarosite transformation in flooded topsoil and subsoils from a rice paddy located on the Bangkok Plain in Central Thailand using an adaptation of the mesh bag method. To test the effect of pore water on the transformation of jarosite in soil, mesh bags were filled with synthetic jarosite and aluminium-jarosite and incubated in topsoils and subsoils, both in laboratory mesocosms and directly in the field. Then, the effect of the soil matrix was tested by completing a parallel experiment using mesh bags containing soil that was pre-enriched with synthetic 57Fe-labelled jarosite and aluminium-substituted jarosite. To facilitate the deployment and collection of small mesh bags in large soil volumes, the mesh bags were inserted into soils using custom-designed 3D-printed sample holders. At three timepoints within twelve weeks, one set of mesh bags were removed from the soil. Transformation products were identified and quantified in the pure jarosite and aluminium-jarosite mesh bags using Rietveld fitting of XRD patterns, while the fate of the 57Fe in enriched soil mesh bags was traced using 57Fe M\u00f6ssbauer spectroscopy. Performing experiments in increasingly complex media provides an insight into the effect of experimental design on the observation of Fe mineral transformations and provides new information regarding the transformation rates and pathways of jarosite and ferrihydrite within full complexity of soil media. Indeed, this thesis demonstrates that the complex chemistry, biological activity, and physical arrangement of components in the soil have strong effects on the rate and products of jarosite and ferrihydrite transformation processes. The transformation of jarosite and Al-substituted jarosite in mixed-suspension experiments presented in this thesis, in agreement with previous mixed-suspension experiments on both jarosite and ferrihydrite, occurred within a matter of hours. By contrast, the rate of ferrihydrite, jarosite and Al-jarosite transformation in soil pore and in direct contact with the soil matrix occurred over the course of several weeks or months. In the ferrihydrite mesh bags, slow ferrihydrite transformation kinetics on the outer rim of the mesh bag, and deep in the core of the mesh bag, indicated that the sorption of chemical components of soil pore water and diffusion limitations of Fe(II) in pore water could be reasons for the slower rates of transformation in soil. In addition, both Al-for-Fe substitution and Fe(II) concentration in solution were important factors that altered the rate of mineral transformation. The different incubation conditions for jarosite and Al-jarosite also altered the products of the transformation. Whereas the hydrolysis of jarosite in the absence of Fe(II) resulted primarily in the formation of ferrihydrite, jarosite transformation in the presence of Fe(II) led to ferrihydrite, goethite and lepidocrocite formation. The Fe oxyhydroxide products were consistent with Fe(II)-catalysed transformation, and Fe(II)-catalysed recrystallisation of jarosite may have occurred concurrently. Aluminium-for-iron substitution hindered the formation of lepidocrocite formation in favour of ferrihydrite and goethite. Similar product phases occurred when jarosite and Al-jarosite were reacted with pore water from acid sulfate soils, indicating that similar transformation pathways may define the mineral products of jarosite transformations when the jarosite occurs as accumulations of pure mineral in soil. However, non- or poorly crystalline phases predominated in the transformation products when jarosite or Al-jarosite were incubated in direct contact with the soil matrix, indicating that the transformation of jarosite under these circumstances was governed by different pathways and processes. The new insights into the transformation of ferrihydrite, jarosite and Al-jarosite in acid sulfate soils demonstrate that phases previously considered meta-stable may participate in the biogeochemistry of soil over period of several months. In the context of rice cultivation, the transformation processes may affect the biogeochemistry of the soils throughout the growing season. The formation of poorly crystalline minerals following the transformation in flooded soils may have positive consequences on the sequestration of other trace and major elements that were associated with the ferrihydrite, jarosite or Al-jarosite prior to the transformation. However, the stabilisation of reduced Fe in the soil matrix may have the opposite effect, promoting the mobility of other ions in solution. The methods used to incubate jarosite and ferrihydrite in soils are easily adaptable to new experimental questions involving the behaviour of Fe-bearing minerals in soil. Therefore, the findings open up a new class of experiments within environmental mineralogy and biogeochemistry, that can help to uncover the processes that occur in the environment and explain the natural variation in the composition of Fe phases in soil.", "keywords": ["jarosite", "iron biogeochemistry", "soil chemistry", "acid sulfate soil", "laboratory study", "ferrihydrite", "soil", "soil incubation", "redox chemistry", "goethite", "iron minerals", "2. Zero hunger", "soil biogeochemistry", "info:eu-repo/classification/ddc/550", "M\u00f6ssbauer spectroscopy", "rice paddy soil", "15. Life on land", "6. Clean water", "Earth sciences", "lepidocrocite", "field study", "13. Climate action", "Raman spectroscopy", "iron oxyhydroxide", "mineral transformation", "iron minerals; mineral transformation; soil; soil chemistry; soil mineralogy; soil biogeochemistry; redox chemistry; iron biogeochemistry; acid sulfate soil; rice paddy soil; jarosite; ferrihydrite; goethite; lepidocrocite; iron oxyhydroxide; M\u00f6ssbauer spectroscopy; Raman spectroscopy; field study; laboratory study; soil incubation", "soil mineralogy"], "contacts": [{"organization": "Grigg, Andrew R.C.", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.3929/ethz-b-000648810"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Thesis/Dissertation", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3929/ethz-b-000648810", "name": "item", "description": "10.3929/ethz-b-000648810", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3929/ethz-b-000648810"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-01-01T00:00:00Z"}}, {"id": "10.5061/dryad.v15dv41vf", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:21:14Z", "type": "Dataset", "title": "Soil biogeochemistry across Central and South American tropical dry forests", "description": "Open AccessWe collected replicated\u00a0soil samples (0-10 cm of mineral soil) from multiple plots in four tropical dry forests in Costa Rica, Mexico, Puerto Rico, and Colombia in the wet and dry season.\u00a0 All samples were analyzed for the following variables in the same laboratory: particle-size distribution, pH, nitrogen mineralization, microbial biomass carbon, microbial biomass nitrogen, microbial biomass phosphorus, soil mineralogy via selective dissolution analyses, soil phosphorus fractionations via a modified Hedley procedure, extracellular enzyme activitities, phospholipid fatty acid profiles and other variables.\u00a0 This dataset reports data for all individual soil samples, i.e. 5 cores per plot, 4 plots per site, for four sites total, in both the wet and dry season.", "keywords": ["580", "550", "13. Climate action", "15. Life on land", "Soil biogeochemistry across Central and South American tropical dry forests"], "contacts": [{"organization": "Waring, B, De Guzman, M, Du, D, Dupuy, J, Gei, M, Gutknecht, J, Hulshof, C, Jelinski, N, Margenot, A, Medvigy, D, Pizano, C, Salgado-Negret, B, Schwartz, N, Trierweiler, A, Van Bloem, S, Vargas G., G, Powers, J,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.v15dv41vf"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.v15dv41vf", "name": "item", "description": "10.5061/dryad.v15dv41vf", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.v15dv41vf"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-01T00:00:00Z"}}, {"id": "10.5683/SP2/2JRHBG", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:23:08Z", "type": "Dataset", "title": "Soil biogeochemistry across Central and South American tropical dry forests", "description": "Open AccessThe availability of nitrogen (N) and phosphorus (P) controls the flow of carbon (C) among plants, soils, and the atmosphere,\u00a0thereby shaping terrestrial ecosystem responses to global change.\u00a0Soil\u00a0C, N, and P cycles are\u00a0linked by\u00a0drivers operating at\u00a0multiple spatial\u00a0and temporal\u00a0scales: landscape-level\u00a0variation\u00a0in\u00a0macroclimate,\u00a0seasonality,\u00a0and\u00a0soil geochemistry;\u00a0stand-scale\u00a0heterogeneity in\u00a0forest composition and\u00a0structure; and microbial community dynamics at the soil pore scale.\u00a0Yet\u00a0in many biomes, we do not know at which scales most of the biogeochemical variation emerges, nor which processes drive cross-scale feedbacks. Here, we examined\u00a0the drivers and spatial/temporal\u00a0scales\u00a0of variation in soil biogeochemistry across four tropical dry forests spanning\u00a0steep gradients of climate, soil parent material, and plant community structure.\u00a0To do so, we quantified soil C, N, and P pools, extracellular enzyme activities, and microbial community structure\u00a0across\u00a0wet and dry seasons\u00a0in sixteen plots located\u00a0in\u00a0Colombia, Costa Rica, Mexico, and Puerto Rico. Soil biogeochemistry\u00a0exhibited marked heterogeneity\u00a0across the sixteen plots, with total organic C, N, and P pools varying four-fold, and inorganic nutrient pools by an order of magnitude.\u00a0Most soil characteristics changed more across space (i.e., among sites and plots) than over time (between dry and wet season samplings). We observed stoichiometric decoupling\u00a0among C, N, and P cycles, which may reflect their divergent biogeochemical drivers. Organic C and N pool sizes were\u00a0positively correlated with\u00a0the relative abundance of ectomycorrhizal trees and legumes.\u00a0By contrast,\u00a0the distribution of\u00a0soil P pools was driven by soil\u00a0geochemistry, with\u00a0larger\u00a0inorganic P pools in soils with P-rich parent material. Most\u00a0earth system\u00a0models assume that\u00a0soils within a texture class\u00a0operate similarly,\u00a0and\u00a0ignore sub-grid cell variation in soil properties. Here we reveal that soil nutrient pools and fluxes\u00a0exhibit as much variation among four Neotropical dry forests as is observed across terrestrial ecosystems at the global scale.\u00a0Thus, the biogeochemical patterns we observed across the Neotropical dry forest biome challenge representation of soil processes in ecosystem models.", "keywords": ["580", "550", "13. Climate action", "15. Life on land", "Soil biogeochemistry across Central and South American tropical dry forests"], "contacts": [{"organization": "Waring, B, De Guzman, M, Du, D, Dupuy, J, Gei, M, Gutknecht, J, Hulshof, C, Jelinski, N, Margenot, A, Medvigy, D, Pizano, C, Salgado-Negret, B, Schwartz, N, Trierweiler, A, Van Bloem, S, Vargas G., G, Powers, J,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5683/SP2/2JRHBG"}, {"rel": "self", "type": "application/geo+json", "title": "10.5683/SP2/2JRHBG", "name": "item", "description": "10.5683/SP2/2JRHBG", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5683/SP2/2JRHBG"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-01T00:00:00Z"}}, {"id": "20.500.11850/648810", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:24:29Z", "type": "Journal Article", "title": "Transformation of jarosite and iron oxyhydroxides in acid sulfate paddy soils", "description": "Open AccessMinerals containing Fe are ubiquitous in soils. By providing an abundance of sites for the sorption and incorporation of major and trace elements, Fe minerals can govern the fate and behaviour of numerous pollutants and nutrients in soils. Furthermore, the reactivity of Fe in redox-dynamic soils produces a web of Fe mineral transformation processes with broad consequences for element cycling. The importance of Fe cycling is no exception in acid sulfate soils, although the high sulfur and low pH conditions produce unique Fe mineral transformation processes and compositions. In acid sulfate soils, jarosite, an Fe-K hydroxysulfate mineral, and ferrihydrite, a common short-range-ordered Fe oxyhydroxide mineral, play a central role in the pedological development of active and post-active acid sulfate soils. Soil pH and the dynamics of metals, such as aluminium, are key to understanding the toxicity of acid sulfate soils and can be directly influenced by jarosite and ferrihydrite transformation processes. Although the transformation of Fe minerals is a key component of biogeochemical processes in redox-active soils, the variables that control the rates and pathways of Fe mineral transformations in soil remain uncertain. The uncertainty arises from the difficulty of tracing molecular processes within a matrix of diverse soil components. Iron minerals are regularly characterised in soils, but the processes that explain the Fe mineral composition of soils cannot be easily resolved. An alternative approach is to perform simplified experiments, such as mixed mineral suspension experiments, under controlled laboratory conditions, to test the effect of individual variables. These systems often use synthetic minerals, although relatively pure jarosite may also be isolated from soils and tested in mixed suspension experiments. While useful to derive mechanistic understanding, the measured outcomes of mixed suspension experiments may not represent the rates and products of transformations that occur in soils. Therefore, the objective of this thesis was to gain new understanding of the stability and transformation of jarosite and ferrihydrite in acid sulfate soils by developing novel experimental techniques to follow the transformation of synthetic jarosite and ferrihydrite directly in soils. The central theme of the thesis is the comparison of jarosite and aluminium-substituted jarosite transformation in experimental media of increasing complexity. The experiments are performed under conditions that are relevant to rice paddy soils because of the importance of rice in global food production, and the unique management of rice paddies whereby regular flooding during the growing season produces distinct redox cycles. In Thailand, large areas of the Chao Phraya River delta are cultivated as rice paddies despite being acid sulfate soils, providing a suitable site to observe the effects of regular redox cycling on the biogeochemistry of Fe minerals in acid sulfate soils. The thesis begins with characterisation of synthetic and natural jarosite mineral composition and reactivity. Spectroscopic techniques (Raman spectroscopy, M\u00f6ssbauer spectroscopy and Energy-dispersive X-ray spectrometry) and X-ray diffraction (XRD) were used to assess the element substitution of mineral samples from two jarosite-alunite synthetic solid solution series. The same characterisation techniques were then applied to a sample of jarosite from an acid sulfate soil in Thailand has a natural Al-for-Fe substitution. The mineral characterisation was followed by a transformation experiment in a mixed-suspension system, similar to experimental designs that have been previously used to study mineral transformation processes. The experiment followed the transformation of the natural jarosite sample from an acid sulfate soil in Thailand and three jarosite samples with variable amounts of Al substitution. The reaction solution mimicked the pH (circumneutral) and Fe(II) content (up to 1:1 ratio of Fe(II) in solution to Fe(III) in solids) of flooded acid sulfate soils. Furthermore, using a 57Fe tracer, the simultaneous transformation processes that explained the distribution of mineral products could be resolved from one another. The transformation experiment revealed the relative reactivity of the minerals in the presence of Fe(II), and created a baseline that could be used to compare traditional mixed-suspension experiments with transformations in complex media such as soil. To advance mineral transformation experiments towards studies in which transformation processes may be followed within a soil matrix, several novel techniques were developed. In a first step, ferrihydrite was incubated for up to twelve weeks in microcosms, each containing 300 g of 5 mM CaCl2 solution and 250 g of one of five paddy soils. The ferrihydrite was buried in the soil within a mesh bag (polyethel terephthalate, 51 \u03bcm pores, 30 mm x 12 mm x 3 mm) that allowed free contact between the synthetic minerals and the pore water, but separated the minerals from direct contact with the soil matrix. The mineral products of the transformation were identified and quantified by Rietveld fitting of XRD patterns. Further, the spatial arrangements of the ferrihydrite and transformation products were measured after two weeks by Raman spectroscopy, which could be used to assess the effects of pore water chemistry and diffusion processes on mineral transformation in the mesh bags. The second step involved measuring jarosite and Al-substituted jarosite transformation in flooded topsoil and subsoils from a rice paddy located on the Bangkok Plain in Central Thailand using an adaptation of the mesh bag method. To test the effect of pore water on the transformation of jarosite in soil, mesh bags were filled with synthetic jarosite and aluminium-jarosite and incubated in topsoils and subsoils, both in laboratory mesocosms and directly in the field. Then, the effect of the soil matrix was tested by completing a parallel experiment using mesh bags containing soil that was pre-enriched with synthetic 57Fe-labelled jarosite and aluminium-substituted jarosite. To facilitate the deployment and collection of small mesh bags in large soil volumes, the mesh bags were inserted into soils using custom-designed 3D-printed sample holders. At three timepoints within twelve weeks, one set of mesh bags were removed from the soil. Transformation products were identified and quantified in the pure jarosite and aluminium-jarosite mesh bags using Rietveld fitting of XRD patterns, while the fate of the 57Fe in enriched soil mesh bags was traced using 57Fe M\u00f6ssbauer spectroscopy. Performing experiments in increasingly complex media provides an insight into the effect of experimental design on the observation of Fe mineral transformations and provides new information regarding the transformation rates and pathways of jarosite and ferrihydrite within full complexity of soil media. Indeed, this thesis demonstrates that the complex chemistry, biological activity, and physical arrangement of components in the soil have strong effects on the rate and products of jarosite and ferrihydrite transformation processes. The transformation of jarosite and Al-substituted jarosite in mixed-suspension experiments presented in this thesis, in agreement with previous mixed-suspension experiments on both jarosite and ferrihydrite, occurred within a matter of hours. By contrast, the rate of ferrihydrite, jarosite and Al-jarosite transformation in soil pore and in direct contact with the soil matrix occurred over the course of several weeks or months. In the ferrihydrite mesh bags, slow ferrihydrite transformation kinetics on the outer rim of the mesh bag, and deep in the core of the mesh bag, indicated that the sorption of chemical components of soil pore water and diffusion limitations of Fe(II) in pore water could be reasons for the slower rates of transformation in soil. In addition, both Al-for-Fe substitution and Fe(II) concentration in solution were important factors that altered the rate of mineral transformation. The different incubation conditions for jarosite and Al-jarosite also altered the products of the transformation. Whereas the hydrolysis of jarosite in the absence of Fe(II) resulted primarily in the formation of ferrihydrite, jarosite transformation in the presence of Fe(II) led to ferrihydrite, goethite and lepidocrocite formation. The Fe oxyhydroxide products were consistent with Fe(II)-catalysed transformation, and Fe(II)-catalysed recrystallisation of jarosite may have occurred concurrently. Aluminium-for-iron substitution hindered the formation of lepidocrocite formation in favour of ferrihydrite and goethite. Similar product phases occurred when jarosite and Al-jarosite were reacted with pore water from acid sulfate soils, indicating that similar transformation pathways may define the mineral products of jarosite transformations when the jarosite occurs as accumulations of pure mineral in soil. However, non- or poorly crystalline phases predominated in the transformation products when jarosite or Al-jarosite were incubated in direct contact with the soil matrix, indicating that the transformation of jarosite under these circumstances was governed by different pathways and processes. The new insights into the transformation of ferrihydrite, jarosite and Al-jarosite in acid sulfate soils demonstrate that phases previously considered meta-stable may participate in the biogeochemistry of soil over period of several months. In the context of rice cultivation, the transformation processes may affect the biogeochemistry of the soils throughout the growing season. The formation of poorly crystalline minerals following the transformation in flooded soils may have positive consequences on the sequestration of other trace and major elements that were associated with the ferrihydrite, jarosite or Al-jarosite prior to the transformation. However, the stabilisation of reduced Fe in the soil matrix may have the opposite effect, promoting the mobility of other ions in solution. The methods used to incubate jarosite and ferrihydrite in soils are easily adaptable to new experimental questions involving the behaviour of Fe-bearing minerals in soil. Therefore, the findings open up a new class of experiments within environmental mineralogy and biogeochemistry, that can help to uncover the processes that occur in the environment and explain the natural variation in the composition of Fe phases in soil.", "keywords": ["jarosite", "iron biogeochemistry", "soil chemistry", "acid sulfate soil", "laboratory study", "ferrihydrite", "soil", "soil incubation", "redox chemistry", "goethite", "iron minerals", "2. Zero hunger", "soil biogeochemistry", "info:eu-repo/classification/ddc/550", "M\u00f6ssbauer spectroscopy", "rice paddy soil", "15. Life on land", "6. Clean water", "Earth sciences", "lepidocrocite", "field study", "13. Climate action", "Raman spectroscopy", "iron oxyhydroxide", "mineral transformation", "iron minerals; mineral transformation; soil; soil chemistry; soil mineralogy; soil biogeochemistry; redox chemistry; iron biogeochemistry; acid sulfate soil; rice paddy soil; jarosite; ferrihydrite; goethite; lepidocrocite; iron oxyhydroxide; M\u00f6ssbauer spectroscopy; Raman spectroscopy; field study; laboratory study; soil incubation", "soil mineralogy"], "contacts": [{"organization": "Grigg, Andrew R.C.", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/20.500.11850/648810"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Thesis/Dissertation", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.11850/648810", "name": "item", "description": "20.500.11850/648810", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.11850/648810"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-01-01T00:00:00Z"}}, {"id": "10.6071/M3C09W", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:23:28Z", "type": "Dataset", "title": "Data from: High-severity wildfire leads to multi-decadal impacts on soil biogeochemistry in mixed-conifer forests", "description": "unspecifiedDuring the past century, systematic wildfire suppression has decreased fire frequency and increased fire severity in the western United States of America. While this has resulted in large ecological changes aboveground such as altered tree species composition and increased forest density, little is known about the long-term, belowground implications of altered, ecologically novel fire regimes, especially on soil biological processes. To better understand the long-term implications of ecologically novel, high-severity fire, we used a 44-y high-severity fire chronosequence in the Sierra Nevada where forests were historically adapted to frequent, low-severity fire, but were fire suppressed for at least 70 years. High-severity fire in the Sierra Nevada resulted in a long-term (44+ y) decrease (>50%, p < 0.05) in soil extracellular enzyme activities, basal microbial respiration (56-72%, p < 0.05), and organic carbon (>50%, p < 0.05) in the upper 5 cm compared to sites that had not been burned for at least 115 y. However, nitrogen (N) processes were only affected in the most-recent fire site (4 y post-fire). Net nitrification increased by over 600% in the most recent fire site (p < 0.001), but returned to similar levels as the unburned control in the 13-y site. Contrary to previous studies, we did not find a consistent effect of plant cover type on soil biogeochemical processes in mid-successional (10-50 y) forest soils. Rather, the 44-y reduction in soil organic carbon (C) quantity correlated positively with dampened C cycling processes. Our results show the drastic and long-term implication of ecologically novel, high-severity fire on soil biogeochemistry and underscore the need for long-term fire ecological experiments.", "keywords": ["soil organic carbon", "soil biogeochemistry", "microbial biomass", "microbial respiration", "13. Climate action", "fire suppression", "15. Life on land", "extracellular enzyme activity", "Sierra Nevada", "mixed-conifer forest", "Nitrogen cycle", "Nitrification", "wildfire"], "contacts": [{"organization": "Dove, Nicholas, Hart, Stephen,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.6071/M3C09W"}, {"rel": "self", "type": "application/geo+json", "title": "10.6071/M3C09W", "name": "item", "description": "10.6071/M3C09W", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.6071/M3C09W"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-20T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=soil+biogeochemistry&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=soil+biogeochemistry&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=soil+biogeochemistry&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=soil+biogeochemistry&offset=9", "hreflang": "en-US"}], "numberMatched": 9, "numberReturned": 9, "distributedFeatures": [], "timeStamp": "2026-07-28T23:07:56.692267Z"}