299 research outputs found
Reactivity of biogenic silica: Surface versus bulk charge density
No full textAcid–base titrations were carried out at three different ionic strengths (0.01, 0.1 and 0.7 M NaCl) on a range of marine and continental biosiliceous materials. The large variability in electrical charging behavior of the various materials is consistent with the existence of two pools of ionizable groups, one on the outer surface of and the other within the silica particles. The relative amounts of internal and external silanols were estimated by fitting a two-site complexation model to excess proton versus pH curves obtained at the different ionic strengths. For fresh diatom frustules and phytoliths, as well as recently deposited biosiliceous sediments, the abundance of internal silanols was of the same order of magnitude as, or exceeded, that of silanols on the external surface. Older biosiliceous materials exhibited lower proportions of internal groups, while a decrease in the relative amount of internal silanols was also observed for diatom frustules artificially aged in seawater. The existence of internal ionizable functional groups explains measured charge densities of biogenic silicas that largely exceed the theoretical site density of silica surfaces. Variations in the relative abundance of internal versus surface silanols further explain the non-uniform dependence of electrical charging on ionic strength, the lack of correlation between total charge density and dissolution kinetics, and the variable 950 cm?1 peak intensity in the infrared spectra of biogenic silicas. Dissolution rates correlate positively with the external charge, rather than the total charge build-up, as expected if dissolution only involves the removal of silicate units from the external surfaces of the particles. The progressive reduction with time of the internal to external silanol concentration ratio represents one of the mechanisms altering the material properties that affect the recycling and preservation of biogenic silica in earth surface environments
Effect of pressure on silica solubility of diatom frustules in the oceans: Results from long-term laboratory and field incubations
No full textThe oceanic cycle of silicon (Si) has been studied extensively due to its close coupling to the oceanic carbon cycle and the biological CO2 pump. The oceanic Si cycle is dominated by the uptake of dissolved silicate (dSi) by planktonic organisms, predominantly diatoms, which use it to synthesize siliceous frustules. As oceanic waters are undersaturated with respect to biogenic silica (bSiO2) the frustules dissolve after death of the organisms, thereby regenerating dSi. Because the dissolution rate of bSiO2 depends on the degree of undersaturation, the thermodynamic solubility of bSiO2 is a key parameter controlling the recycling efficiency of nutrient Si in the water column and sediments. While an extensive body of data exists describing the dependence of bSiO2 solubility on temperature, the effect of pressure on the solubility of natural diatom frustules has never been measured directly. In this study, we conducted long-term (up to 22 months) laboratory and field equilibration experiments to determine the solubility of cleaned frustules of a cultured marine diatom (Thalassiosira punctigera) in seawater, for pressures between 1 and 700 bar, and temperatures between 2 and 21 °C. According to our results, the solubility of the frustules decreases by about 10% when pressure increases from 1 to ~ 200 bar. From 200 bar on, the pressure dependence reverses, and at 700 bar the solubility is about 15% higher than at atmospheric pressure. Integrated over an average oceanic water depth of 4000 m, a drop in temperature of 15–20 °C has a far more significant effect on the solubility of bSiO2 than a corresponding 400 bar increase in pressure
Energetic scaling in microbial growth_data
No full textHere leveraging decades of experimental data on growth of microbial isolates, we study in depth the non-equilibrium thermodynamics of microbial growth to shed light on the relation between mass and energy constraints on growth. Our results show that there exist universal scaling laws relating the thermodynamic efficiency of microbial growth to the electron donor uptake rate and to the growth yield, which tightly couple mass and energy conversion in microbial growth. This resource contains an excel file with original data from Smeaton and Van Cappellen (2018) and the thermodynamic calculations for the article associated to this resource, and a Mathematica code used for drawing the Figures
Seawater-mediated interactions between diatomaceous silica and terrigenous sediments: Results from long-term incubation experiments
No full textReactors containing frustules of the cultured diatom Thalassiosira punctigera suspended in seawater were
incubated with or without added sediment from the Mississippi River Delta or the Congo River Fan. The
diatom frustules were separated from the terrigenous sediments by a dialysis membrane, thereby only
allowing the exchange of dissolved species. One series of incubations was carried out in the laboratory, at
room temperature (21 °C) and for a period of 10 months. Another series of reactors was deployed along a
mooring in the Mozambique Channel at three water depths (500, 1250, and 2000 m), for a period of
22 months. Chemical analyses after total destruction of frustules collected at the end of the incubations
showed elemental transfer from seawater (Mg and K) and the sediments (Al, Fe, Mn, P and Ca) to the
frustules. In the presence of the terrigenous sediments, the dissolved silicate concentrations at the end of the
incubations were systematically lower that those measured in the incubations without the sediments. In
addition, electron microscopy revealed the formation of new mineral precipitates. These included
amorphous deposits on the frustules containing Si, Fe, Al, Mg, K and P, as well as euhedral clay crystallites.
Differences were observed between the incubations performed in the laboratory and those deployed at sea,
likely as a result of differences in redox conditions, temperature and reaction time. Overall, the interactions
between biogenic silica, seawater and lithogenic minerals reduce the regeneration of nutrient silicon fixed by
siliceous organisms. These interactions take place on relatively short time scales (months to years), and
affect not only the marine cycle of silicon, but also those of other major and minor elements, such as Al, Fe,
Mn, K, and Mg
Phosphorus Legacies and Water Quality Risks: A Vulnerability-Based Framework in Southern Ontario
No full textExcess phosphorus (P) loading increases the frequency of harmful algal blooms (HABs), posing severe threats to drinking water security and aquatic ecosystems. Efforts to reduce the inputs of P to Canadian agricultural soils started in the late 1970s-early 1980s, and were initially successful, but surface water P loading became persistent again in the 2000s. HABs were a problem in the southern Laurentian Great Lakes (LGL) before the initial nutrient mitigation efforts, and the re-emergence of HABs in Lake Erie in the 2000s was in part a result of legacy P that had accumulated in soils and groundwater in agricultural watersheds. Legacy P exists as a result of historical inputs of P, typically fertilizer used in excess of crop needs. Consequentially, even after reducing P inputs, legacy P continues to be exported from soils after several decades. In Chapter 2, a large-scale mass balance was conducted for the Ontario watersheds to locate and quantify agricultural and other anthropogenic P inputs from 1961 to 2016, utilizing existing datasets as well as historical reconstructions of P inputs to the landscape. This scale of P mass-balance has not been completed before in Ontario. The mass balance model was implemented into a Geographical Information System (GIS) platform to delineate potential areas with legacy P accumulation and depletion within the landscape. These maps identified areas with high P inputs and large potential stores of legacy P. Historically, southwestern Ontario has had the densest agriculture and populated areas in Ontario and has had high P inputs over time. County-scale trends such as shifts to intensive livestock or crop-based agriculture, or increasing urbanization were also identified. In Chapter 3, the fate and transport of P and the possible development of P legacies was explored in the context of risk. P export is influenced by environmental conditions in soil, as such, there is spatial variance in the likelihood that P will runoff or accumulate in soils. The environmental conditions may therefore be used to represent the vulnerability of the system and the risk to either lose or accumulate P. The cumulative agricultural P surplus map was used in conjunction with vulnerability maps to construct soil P risk maps. Different vulnerability models were explored, and ultimately soil erosion potential maps were used to identify vulnerable areas with a high risk of P losses to surface water and areas with a high risk of P accumulation in soil. It was determined that there was a higher risk of P accumulation in soil along the coast of Lake Erie, and it is possible that P legacies exist in these areas. The results inform nutrient management and abatement strategies and the adaptive implementation of conservation practices
Degradation of Polyethylene Terephthalate (PET) and Polyamide (PA)
No full textMicroplastics have become an increasing concern to humans and ecosystems as plastic production continues to soar, due to their prevalence in the environment and lifespan. Plastic is cheap and durable making it an ideal industrial and commercial material. However, because of this popularity, it resides in most places on earth, including in human blood, and is difficult to remove due to its small size. These plastics can enter the environment through numerous methods, from landfills and dumps to washing machines and sinks. In recent years, there has been significant investigation in reducing plastic pollution. This a difficult task attributed to the varying size, shape, polymer type, chemical properties and location plastic can be found. It’s critical to understand the rate of degradation and the factors that influence it for two main reasons; it provides accurate timelines of degradation and techniques that may increase degradation need a starting point.
In Chapter 2, I investigate the degradation rate of laboratory grade polyethylene terephthalate (PET) using a model enzyme (Huimcola insolens cutinase) to hydrolyze the plastic. This research aims to characterize the polymers used such that results can be compared and identify the analyses which capture degradation and characterize the polymer best. Environmental factors controlling enzymatic plastic degradation are not well studied and this experiment aimed to study the effect of incubation temperature, exposure to freeze-thaw cycles (FTCs) and extreme temperatures on the degradability of laboratory-grade PET. In addition, we also assessed the degradability of consumer-grade PET, sourced from plastic bottles, for comparison to the laboratory-grade PET. The first test was under variable temperatures, where plastic was incubated at 25 ˚C, 40 ˚C and 55 ˚C. The results show increased temperatures increase the rate of polymer degradation. The second set of tests were conducted under different pretreatments; treatments the plastic would undergo before incubation at 40 ˚C. Plastic was exposed to a series of freeze-thaw cycles (FTCs) or extreme temperatures (-70 ˚C or +55 ˚C). It was found any type of pretreatment increased the rate of degradation compared to plastics that did not undergo any pretreatment. The final condition tested was plastic type, where PET water bottles were obtained and incubated at 55 ˚C to determine the differences in degradability between laboratory-grade PET and consumer-grade PET. Consumer-grade PET was found to not have any significant degradation after 10 weeks of enzyme exposure, raising serious concerns regarding its degradability and lifespan. This result suggests that modifications to the consumer-grade PET during the fabrication process, such as heat treatments, are altering its chemistry and its degradation kinetics. Analyses for degradation and characterizing the polymers included: Fourier-transform infrared (FTIR) spectroscopy, differential scanning calorimetry (DSC), scanning electron microscopy (SEM) and tensile strength measurements. Analysis of the crystallinity, tensile strength, SEM images and FTIR spectra measured indicate that PET’s physical and chemical properties were modified when degraded. Overall, the PET’s tensile strength decreased and the crystallinity increased with increasing hydrolytic degradation. FTIR spectral changes were seen early on, with peaks of interest at 1237 cm-1, 1016 cm-1 and 1087 cm-1, and finally at 1716 cm-1, and the flattening of these peaks increased with increasing hydrolytic degradation. The results highlight that enzymatic degradation rates can be highly variable due to differences in environmental conditions. It also highlights the large difference in the degradability of consumer-grade versus laboratory-grade PET, which has significant implications for in situ environmental degradation rates.
In Chapter 3, I investigated the rate of laboratory-grade PET and polyamide (PA) degradation in stormwater pond sediment over a 16 month period in a stormwater pond in Kitchener, Ontario. Microplastic accumulation in the environment, especially in bodies of water and sediment is a well-known problem. Stormwater ponds act as a microplastic sink and draw pollutants from urban and industrial wastewater before it enters oceans or lakes. This results in high levels of microplastics remaining in stormwater pond sediment. Stormwater ponds are an excellent site to determine realistic plastic degradation in the environment, in a contained area where high concentrations of plastic is known to be present. To date, no long-term polymer degradation studies have been conducted in a stormwater pond despite the rising popularity of these ponds. For this study, 8 pore water samplers (peepers) were packed with pond sediment and plastic pieces were inserted into each cell of the peeper. An additional 8 peepers filled with water, such that pore water chemistry could be collected. The peepers were inserted into the pond sediment and sacrificed periodically over the course of 16 months. For the first 8 months both PET and PA plastic increased in mass as they absorbed water. After 16 months of field incubation, PA had degraded by 0.42% and PET was still net positive (higher mass than before the incubation) however it was close to its original weight. The obtained results highlight the lack of degradation to plastics in stormwater pond sediment and suggest lifespans are longer than previously estimated. Based on previous degradation studies under sediment conditions, this study suggests that stormwater pond sediment is the least effective at degradation polymers, which may be attributed to the pond water chemistry and microbial communities present. Microplastics are known to accumulate in stormwater pond sediment but they are found to degrade at slower rates than other sediment profiles. The laboratory experiment results in Chapter 2 show under ideal conditions laboratory-grade PET degrades minimally at low temperatures. Additionally, the lack of degradation seen with the consumer-grade PET in Chapter 2 suggests that under environmental conditions, the polymer would take even longer than the laboratory-grade polymers to degrade. The combination of Chapter 2 and 3 demonstrate the difference between ideal and environmental conditions for polymer degradation. This research provides evidence to strongly advocate for the removal of microplastics before they enter the environment as I have proven they take considerable lengths of time to degrade under various conditions. I encourage this research to be used by any future researchers who hope to develop methods for plastic pollution reductions
Perturbations to nutrient and carbon cycles by river damming
No full textThe damming of rivers represents one of the most far-reaching human modifications to the flows of water and associated matter from land to sea. Globally there are over 70 000 large dams whose reservoirs store more than seven times as much water as natural rivers. Due to increasing demands for energy, irrigation, drinking water, and flood control, the construction of dams will continue into the foreseeable future. Indeed, there is currently an ongoing boom in dam construction, particularly focused in emerging economies, which is expected to double the fragmentation of rivers on Earth. Essential nutrient elements such as phosphorus (P), nitrogen (N), silicon (Si), and carbon (C) are transported and transformed along the land-ocean aquatic continuum (LOAC), forming the basis for freshwater food webs in lakes, rivers, wetlands, reservoirs, and floodplains, and ultimately for marine food webs in estuarine and coastal environments. The dam-driven fragmentation of the rivers along the LOAC will significantly modify global nutrient and C fluxes via elimination from the water column in reservoirs.
In this thesis, I quantify in-reservoir elimination and transformation fluxes for phosphorus (P), silicon (Si), and organic carbon (OC), with the goal of determining (1) how much Si, P, and organic C (OC) are retained or eliminated globally due to river damming, (2) how damming modifies the balance of productivity (heterotrophy vs. autotrophy) in river systems worldwide, (3) to what extent damming changes nutrient speciation or reactivity along the LOAC, and (4) if reservoirs retain or eliminate certain nutrients more efficiently than others, and if so, how this decoupling changes nutrient ratios delivered to coastal zones. I address these research questions at the reservoir scale, by quantifying nutrient elimination in Lake Diefenbaker, Saskatchewan, and through the development of spatially explicit global nutrient and carbon models.
In Chapter 2, I present a reservoir-scale field study of reactive silicon dynamics in Lake Diefenbaker, a reservoir in Canada’s central prairie province of Saskatchewan. I use a year-round dataset of surface water samples and sediment cores to construct a Si budget for the reservoir, including an estimation of the amount of Si buried in the reservoir annually. I use this study to illustrate the differences in retention of Si relative to N and P, and put forth the hypothesis that river damming results in a decoupling of nutrient cycling. This study acts as an introduction to the concept of differential nutrient retention in reservoirs, which I go on to show at the global scale for Si, P, and C in reservoirs in Chapters 3, 4, and 5.
Following Chapter 2, I address my research questions by developing a mechanistic approach to global scale biogeochemical modelling. This approach yields spatially explicit results, which allows for the quantification of regional watershed and coastal trends, as well as lumped continental changes. In Chapter 3, the modelling approach itself is introduced, through application to the Si cycle. I show, via a meta-analysis comparing the distribution of physical and chemical parameters of published reservoir Si budgets to reservoirs worldwide, that the existing literature Si budgets are severely limited in their ability to represent the dataset of global reservoirs. I then introduce the mechanistic approach by developing a biogeochemical box model representing Si dynamics in reservoirs. I assign rate expressions to transformation fluxes and input/output fluxes, which are constrained as uniform distributions between limits that encapsulate possible global ranges. Using a Monte Carlo approach, I allow the model to randomly select each rate constant independently for 6000 iterations, generating a database of hypothetical Si dynamics in reservoirs worldwide. I use this generated dataset to establish expressions relating Si retention to water residence time, which I apply to an existing database of global reservoirs. Ultimately I develop a global estimate of dissolved and reactive Si burial in reservoirs for year 2000.
Chapters 4 and 5 use the same modelling approach presented in Chapter 3, but applied to riverine P and organic carbon (OC) fluxes. Because the cycles of P and OC have been studied in more detail than Si in the literature, it is possible to constrain higher order probability density functions (PDFs) for many rate constants. In the case of OC, it also becomes possible to use a statistically significant semi-empirical approach to calculate a number of fluxes, as expressions to predict OC dynamics have been established from globally applicable datasets. Using the upstream-catchment area-normalized Global-NEWS model’s watershed yields as input to each reservoir, I use the 1970, 2000, 2030 and 2050 model predictions to estimate historical and predict future P and OC elimination by dams. In Chapter 4, I show that damming retains 12% of the global total P load to watersheds in year 2000, potentially rising to 17% by 2030. In Chapter 5, I show that global OC mineralization in reservoirs exceeds carbon fixation (P<R); the global P/R ratio, however, varies significantly, from 0.20 to 0.58 because of the changing age distribution of dams. I further estimate that at the start of the 21st Century, in-reservoir burial plus mineralization eliminated 4.0 ± 0.9 Tmol yr-1 (48 ± 11 Tg C yr-1) or 13% of total OC carried by rivers to the oceans. Because of the ongoing boom in dam building, in particular in emerging economies, this value could rise to 6.9 ± 1.5 Tmol yr-1 (83 ± 18 Tg C yr-1) or 19% by 2030.
Chapter 6 ties the previous global scale P and Si model together, plus a global scale N model (Akbarzadeh et al., in preparation), to predict changes to nutrient ratios delivered by rivers to the coastal zones. I use this analysis, in combination with anthropogenic nutrient loading data, to contextualize the role of river damming as a driver of changing nutrient limitation in the coastal shelf zones of the world. Results indicate that dams preferentially eliminate P over Si, and Si over N, from the water column. I show that while damming drives riverine N:P ratios up, anthropogenic nutrient loading is shifting these ratios down, increasing the prominence of N-limitation in river water discharged to the coasts. Because of the preferential elimination of Si over N, the net rise in N-limitation increases the prominence of Si-limitation in coastal river discharge, potentially creating conditions suitable for harmful algal blooms to develop.
My results show that damming is driving a severe reorganization of global nutrient cycles along the entire LOAC. By quantifying the changes to multiple nutrient cycles, I show that a multi-nutrient management approach is needed in heavily dammed watersheds, as deliberate reduction of one nutrient species flux can have unintended consequences on other nutrient elements. These alterations persist from the reservoir to the river’s discharge into coastal zones. The effects of damming on nutrient cycling, in combination with other human pressures and management strategies, therefore have the potential to affect ecosystems worldwide
Modeling Phosphorus Cycling in a Seasonally Stratified Reservoir (Fanshawe Reservoir, Ontario, Canada)
No full textHuman activities, such as mining, sewage discharge, fertilizer usage and dam construction for electricity and flood controll, have significantly disturbed the biogeochemical cycling of nutrients, such as carbon, phosphorus, and nitrogen, in atmospheric, terrestrial, and aquatic systems. Globally, negative effects of the excess inputs of nutrients have been observed in freshwater and saline surface water environments. Phosphorus (P) is an essential nutrient for primary production, and due to intensive anthropogenic activities, including rapid agricultural intensification and urban development, excess P has been loaded into the Thames River Watershed (TRW), Ontario, Canada for around 45 years. Water quality in the TRW has been significantly affected by inputs of P and other nutrients. These eutrophic waters could have significant and chronic negative effects on the downstream and nearby aquatic environment, such as Lake St. Clair and Lake Erie. This thesis focuses on Fanshawe Reservoir, located in the Northern TRW, where Fanshawe Dam has been built to control potential flood events that may damage the City of London. However, excess nutrients could accumulate in the reservoir sediments and slowly release over a long period, posing significant difficulties for water quality management. During summertime, blue-green algae and elevated bacterial concentrations have been frequently observed by the Upper Thames River Conservation Authority (UTRCA). However, the existing field data cannot explain the seasonal variation of the algal blooms or the long-term scale interaction between the external loading of P and internal loading of P. To provide a computational framework to analyse existing field data and relate P availability in Fanshawe Reservoir to external and internal P loading, I developed a two-dimensional model for Fanshawe Reservoir using the CE-QUAL-W2 software. The model combines hydrodynamic, water quality, and sediment diagenesis modules. The simulation results imply a major role of internal P loading during the summer when the reservoir stratifies. Retention of P mainly occurs during wintertime, while the reservoir is a source of P during summertime. In a scenario where external P input to the reservoir is instantaneously reduced by 40%, the annual downstream export of P from the reservoir only decreases by 22%, because of continued internal P loading from the sediments. Due to the legacy P stored in the sediments, it would take on the order of 22 years for P export from Fanshawe Reservoir to drop to 36.5% of its current value. In another biomass scenario, the sediment P loading has 40.1% larger effects on algal growth than the external loading of P during summertime. Furthermore, to provide feasible and fast water quality modeling applications, a back propagation artificial neural network (BP-ANN) model was successful developed and calibrated for the future modeling works
Tracing Redox Cycles during Microbe-Clay Interactions Using Stable Iron Isotopes
No full textIron redox cycling, especially Fe(III) reduction, is mostly driven by microbial activity in the shallow subsurface. A wide range of bacteria, archaea, and fungi reduce Fe(III) to acquire energy with soil organic compounds as the electron donors. Iron isotope signatures in ancient rocks (3.1-2.4 Ga) associated with dissimilatory Fe reduction (DIR) have been interpreted in terms of global changes in oceanic redox condition. Iron isotopes have also been used as indicators of redox processes involving Fe minerals such as Fe(III) (oxyhydr)oxides and pyrite. Clay minerals, however, contain approximately the same amount of Fe as all other Fe minerals combined, thereby playing a key role in Fe redox cycling. There have been numerous studies focusing on the mineralogical changes of clays during microbially, chemically, and electrochemically mediated redox cycles, and linking these changes to the bioavailability and reversibility of clay, including processes such as layer collapse, structural Fe migration, and dehydroxylation and water fixation. I used Fe isotopes, for the first time, to trace the redox cycling of clay minerals. Model nontronite minerals NAu-1 and NAu-2 were purified prior to the experiments to exclude impurities such as Fe oxides, kaolinite, and quartz. The purity of NAu-1 and NAu-2 was checked with X-ray diffraction (XRD) and scanning electron microscopy (SEM) coupled to energy dispersive spectroscopy (EDS), and transmission electron microscopy (TEM).
In Chapter 2, I present Fe isotope fractionations measured during the microbial reduction, chemical reduction, and mixing experiment of nontronite NAu-1. Microbial (Shewanella oneidensis MR-1 and Geobacter sulfurreducens PCA) and chemical (dithionite) reduction of NAu-1 produced isotopically lighter aqueous Fe(II) during the early stage of the reduction, with maximum isotope fractionation factors between aqueous Fe(II) and structural Fe(III) from -1.2 to -0.8‰. Iron isotope fractionation was produced by the electron transfer coupled atom exchange (ETAE) between aqueous Fe(II) and structural Fe(III) via the adsorbed Fe(II) on edge sites. With microbial reduction proceeding to the extent at which structural Fe(II) fully covered the edge surface of NAu-1, isotope fractionation between aqueous Fe(II) and structural Fe(III) decreased to ~0‰ due to a lack of ETAE. Meanwhile, minor ETAE continued between edge-bound Fe(II) and structural Fe(III). The variation of Fe isotope fractionation was coupled to the reduction of bioavailable structural Fe(III), which represented ~10% of the total Fe in NAu-1, showing that Fe isotopes can be useful tracers of Fe redox changes in clay minerals.
On the basis of the results of Chapter 2, in Chapter 3 I exposed NAu-1 and S. oneidensis MR-1 to three successive redox cycles to assess the redox reversibility of bioavailable Fe in NAu-1. Each redox cycle consisted of a long biotic reduction period (RP) and a short abiotic oxidation period (OP), between which the dissolved Fe(II) was removed to minimize the formation of Fe(III) (oxyhydr)oxides. Secondary mineral formation was not detected during the redox cycles. The initial fraction of bioavailable Fe in the unaltered NAu-1 was ~10% as proposed in Chapter 2. The remaining bioavailable Fe decreased from RP1 to RP3 due to the removal of the dissolved bioavailable Fe during the preceding RP. The dissolution of bioavailable Fe was primarily generated by the reduction of the smallest NAu-1 particles, while bioavailable Fe in the larger particles remained within the solid upon reduction. Due to the consumption of the small particles, bioavailable edge surface where ETAE takes place decreased with successive RPs, as implied by the decreasing Fe isotope fractionation from RP1 to RP3. By extrapolating the linear relationship between the extent of Fe(III) reduction and the fraction of dissolved Fe(II), I predict that ~4.2% of the total Fe in NAu-1 is redox reversible upon continued redox cycling, while ~5.8% of the total Fe is removed into solution.
In Chapter 4 I examine the bioavailability of Fe in a tetrahedral Fe(III)-containing nontronite (NAu-2) via microbial (S. oneidensis MR-1) and chemical reduction (dithionite). The microbial reduction of NAu-2 exhibited three stages according to the change in isotope fractionation between different Fe pools [i.e., aqueous Fe(II), basal-sorbed Fe(II), edge-bound Fe, structural Fe]: 1) stage 1 was characterized by increasing isotope fractionation between aqueous Fe(II)/edge-bound Fe and structural Fe, indicating ETAE mainly occurred along the edge surface of NAu-1; 2) at medium to high reduction extent, stage 2 exhibited decreasing isotope fractionation between edge-bound Fe and structural Fe, while the fractionation between aqueous Fe(II)/basal-sorbed Fe(II) and structural Fe further increased, implying that the edge surface was blocked and prevented ETAE (that is, from then on ETAE mainly occurred on the basal plane surface); 3) Fe reduction reached its maximum extent during stage 3, while the isotope fractionation between aqueous Fe(II)/basal-sorbed Fe(II) and structural Fe decreased, indicating that the ETAE through the basal planes became inhibited. The observed iron isotope fractionations show that NAu-2 has increased exchangeable basal plane redox reactivity due to the presence of tetrahedral Fe(III). The reactive basal plane surface may be particularly important under acidic condition, because, under low pH, cation adsorption mainly takes place on the basal planes.
Overall, my results show that Fe isotopes are a useful tool to study the Fe redox reversibility of clay minerals during redox cycles. However, on the basis of my results, I propose that microbial reduction of Fe(III) in clay may not have contributed to the isotope signatures recorded in BIFs during the late Archean. In addition, the presence of tetrahedral Fe may enhance the reactivity of clay minerals towards redox-active contaminants
Bioenergetics of mixotrophic metabolisms: A theoretical analysis
No full textMany biogeochemical reactions controlling surface water and groundwater quality, as well as greenhouse gas emissions and carbon turnover rates, are catalyzed by microorganisms. Representing the thermodynamic (or bioenergetic) constraints on the reduction-oxidation reactions carried out by microorganisms in the subsurface is essential to understand and predict how microbial activity affects the environmental fate and transport of chemicals. While organic compounds are often considered to be the primary electron donors (EDs) in the subsurface, many microorganisms use inorganic EDs and are capable of autotrophic carbon fixation. Furthermore, many microorganisms and communities are likely capable of mixotrophy, switching between heterotrophic and autotrophic metabolisms according to the environmental conditions and energetic substrates available to them. The potential for switching between metabolisms has important implications for representing microbially-mediated reaction kinetics in environmental models. In this thesis, I integrate existing bioenergetic and kinetic formulations into a general modeling framework that accounts for the switching between metabolisms driven by either an organic ED, an inorganic ED, or both.
In Chapter 2, I introduce a conceptual model for mixotrophic growth. The conceptual model combines the carbon and energy balances of a cell by accounting for the allocation of an organic ED between incorporation into biomass growth and the generation of energy in catabolism. I select experimental datasets from the literature in which mixotrophic growth of pure culture organisms is assessed in chemostats. These experiments employ biochemical methods that allow one to estimate the contributions of the possible end-member metabolisms under variable supply rates of organic and inorganic EDs. Using the conceptual model, I develop a quantitative modeling framework that explicitly accounts for the substrate utilization kinetics and the energetics of the catabolic and anabolic reactions. I then compare the model predictions to the experimental data.
While in Chapter 2 datasets collected in controlled laboratory settings are considered, in Chapter 3 I apply my modeling framework for mixotrophic growth to a lake sediment geochemistry dataset. I focus on the activity of a nitrate reducing, acetate and iron(II) oxidizing mixotrophic microbial community in the suboxic zone of the lake sediment. I demonstrate the application of the modeling framework to this natural system, based on the reported concentration profiles of the relevant EDs (i.e., acetate and iron(II)), electron acceptors (EAs) (i.e., nitrate), and other reactants and products to calculate the depth distributions of the energetic and kinetic constraints in the model calculations. The predicted fractions of the metabolic end-members are in general agreement with the relative distributions of the different microbial functional groups reported in the original study. I also assess the sensitivity of the model’s predictions on the kinetic parameter values used to simulate the net utilization rates of the two EDs. The results of the analysis provide new insights into the role of mixotrophy in the coupled cycling of nitrogen, iron(II), and dissolved inorganic carbon in the nitrate-reducing zone of lake sediments.
The conceptual model and modeling framework presented in this thesis can be used to account for mixotrophic activity in environmental reactive transport models. That is, in the future, this modeling framework could be incorporated into models that simulate the interactions of mixotrophy with other geochemical, geomicrobial, and transport processes. The work presented in this thesis is thus a valuable step towards building realistic theoretical representations of microbial activity in earth’s near surface environments
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