In this study we investigated the effect of tidal forcing on iron cycling in intertidal saltmarsh sediments (ISS). Historically, sulfate has been considered the major terminal electron acceptor involved in organic carbon remineralization in ISS. Although sulfate is a more efficient electron acceptor for organic matter degradation in anoxic ISS, irons rapid recycling at the surface of ISS may allow it also to be an important electron acceptor for the remineralization of organic matter. Bioturbation, macrophyte-mediated irrigation, and semidiurnal tidal forcing in this environment may increase the abundance of O2 in the top few cm of the sediment, rapidly oxidizing iron and inhibiting sulfate reduction. To determine if the cycling of iron may be faster than previously thought in these sediments, we combined sediment core chemical profiles of reduced and oxidized insoluble iron with in-situ electrochemical profiles of O2, Fe2+, soluble organic-Fe3+ complexes, FeS(aq), and hydrogen sulfide in the top few centimeters of unvegetated creek bank sediments over several tidal cycles. We also installed monitoring wells in the tidal creek bank to quantify tidal forcing and to investigate tidal direction in the sediments. We built a transient, reactive transport model to simulate measured geochemical profiles and test our understanding of diagenetic processes. Additional tests were run on the model to investigate the importance of bioirrigation compared to tidally-induced porewater advection. Results indicate that tidal action is a more dominant transport process. It affects the cycling of iron in ISS by flushing reduced species out of the sediment during flood tide, and allowing oxygen and oxidized species deeper into the sediment during ebb tide. As a result, amorphous iron oxides are replenished at the sediment surface, and microbial iron reduction may be the main respiratory process in the first tens of centimeters of creek bank saltmarsh sediments subjected to intense tidal forcing.

The complex interactions at the interfaces of minerals, microbes, and metals drive the cycling of iron and the fate and transport of metal(loid)s in contaminated systems. The former uranium mine near Ronneburg, Germany is one such system, where slightly acidic mine drainage crossing a steep redox gradient (groundwater outflow into a stream) forms and transforms iron (oxy)hydroxide nanoparticles. These particles interact with toxic metal(loid)s in water and sediments. Iron oxidizing and reducing bacteria also play a role in these processes. Biogeochemical reactions are influenced by nanoscale properties, and thus it is critical to probe environmental samples with appropriate techniques such as analytical transmission electron microscopy (TEM). This dissertation presents two studies on the iron (oxy)hydroxide mineral nanoparticles found in the Ronneburg mine drainage system. The first study uses TEM in conjunction with bulk analytical techniques to demonstrate the complexity of iron (oxy)hydroxide transformations at the steep redox gradient, and the partitioning of metal(loid)s within those mineral phases. An important result was the identification of Zn-bearing green rust platelets in the anoxic outflow water. Green rust minerals have only been identified in nature a handful of times, and we believe this work to be only the second to examine naturally occurring green rust using high resolution TEM (HR-TEM). Downstream of the outflow, aggregates of poorly crystalline iron oxide spheroids co-precipitated with amorphous silica formed and settled to the stream bed, where they aged to form nanoparticulate goethite and sequestered metals such as As and Zn. However, significant concentrations of Zn and Ni remained in the dissolved/nano (< 0.1 um) water fraction and continued downstream. The second study demonstrates that natural green rust nanoparticles and their synthetic analogs can be complex polycrystalline phases composed of crystallites only a few nanometers in size, and often include nano-regions of amorphous material. In addition to the typical pseudo-hexagonal platelet morphology, green rust nanorods were synthesized, which has not previously been reported. This work has important implications for the reactivity of green rust with biogeochemical interfaces in natural, anthropogenic, and industrial systems. A third study, presented in the appendix, characterizes the bacterial community at the Ronneburg mine drainage site and highlights iron oxidizers such as Gallionella sp., in particular those that form stalks of iron oxide nanoparticles. These biogenic stalks also contribute to the uptake of metal contaminants in water and sediments. The science of iron cycling is complex. It requires field-based exploration to enrich the contributions made by experimental, laboratory and modeling studies. This dissertation adds another chapter in the search for filling in missing pieces of this interconnected system. / Ph. D.

Fe biofortification of potato is a promising strategy to prevent Fe deficiency worldwide either through traditional breeding or biotechnological approaches. These approaches require the identification of candidate genes to uptake, transport and store Fe in potato tubers. We employed multiple approaches including SNP genotyping, QTL analysis, identifying genes orthologous to Arabidopsis ferrome, yeast complementation assay and genetic transformation to avoid the limitation from a single approach. We revealed several candidate genes potentially associated with potato plant Fe acquisition, PGSC0003DMG400024976 (metal transporter), PGSC0003DMG400013297 (oligopeptide transporter), PGSC0003DMG400021155 (IRT1) and IRTunannotated (an ortholog to the IRT gene that is not annotated in the potato genome). The microorganisms in the rhizosphere react intensely with the various metabolites released by plant roots in a variety of ways such as positive, negative, and neutral. These interactions can influence the uptake and transport of micronutrients in the plant roots. Therefore, the contribution of soil microorganisms in the rhizosphere to improve Fe supply of plants may play a key role in Fe biofortification, especially under real world field-based soil scenarios. We thus investigated rhizosphere microbial community diversity in Andean potato landraces to understand the role of plant-microbial interaction in potato Fe nutrient cycling. From the analysis of the high-throughput Illumina sequences of 16S and ITS region of ribosomal RNA gene, we found that both potato landraces with low and high Fe content in tubers and a landrace on which low or high Fe content fertilizer was applied to the leaf surface had large impacts on the rhizosphere fungal community composition. Indicator species analysis (ISA) indicated that Operational Taxonomic Units (OTUs) contributing most to these impacts were closely related to Eurotiomycetes and Leotiomycetes in the phylum Ascomycota, Glomeromycetes in the phylum Glomeromycota and Microbotryomycetes in the phylum Basidiomycota. Lots of species from these groups have been shown to regulate plant mineral nutrient cycling. Our research revealed potential candidate genes and fungal taxa involved in the potato plant Fe nutrient dynamics, which provides new insights into crop management and breeding strategies for sustainable Fe fortification in agricultural production. / Ph. D. / Sustainably enriching Fe nutrition and its bioavailability in the potato is a promising strategy to prevent Fe deficiency worldwide either through traditional breeding or biotechnological approaches. All of these approaches require the identification of candidate genes to uptake, transport and store Fe in potato tubers. In this study, we coupled plant molecular methods with analysis of soil microbial community in the rhizosphere (the region of soil within immediate vicinity of plant roots, and a hotspot of this plant-microbial interplay) to uncover relationships among Fe nutritional status in potato, potato genotype and soil microbes. We identified a number of genes that likely control the amount of Fe content in potato using multiple approaches. After functional analysis in yeasts and potato plants, we revealed several elite candidate genes potentially associated with potato plant Fe acquisition, <i>PGSC0003DMG400024976</i> (Metal Transporter), <i>PGSC0003DMG400013297</i> (Oligopeptide Transporter), <i>PGSC0003DMG400021155</i> (Iron-Regulated Transporter 1, IRT1) and <i>IRTunannotated</i> (an ortholog to the <i>IRT</i> gene that is not annotated in the potato genome). The microorganisms in the rhizosphere react intensely with the various metabolites released by plant roots in a variety of ways such as positive, negative, and neutral. These interactions can influence the uptake and transport of micronutrients in the plant roots. Therefore, the contribution of soil microorganisms in the rhizosphere to improve Fe supply of plants may play a key role in enriching Fe nutrition, especially under real world field-based scenarios, e.g., high-pH and calcareous soils that occupy one third of agriculture lands limit the Fe bioavailability to crops. We investigated rhizosphere microbial community diversity in Andean potato landraces to understand the role of plant-microbial interaction in potato Fe nutrient cycling using high-throughput Illumina sequencing method. We found that both potato landraces with low and high Fe content in tubers and a landrace on which low or high Fe content fertilizer was applied to the leaf surface had large impacts on the rhizosphere fungal community composition. These impacts were closely related to <i>Eurotiomycetes</i> and <i>Leotiomycetes</i> in the phylum <i>Ascomycota, Glomeromycetes</i> in the phylum <i>Glomeromycota</i> and <i>Microbotryomycetes</i> in the phylum <i>Basidiomycota</i>. Lots of species from these groups have been shown to regulate plant mineral nutrient cycling. Our research revealed potential candidate genes and fungal taxa involved in the potato plant Fe nutrient dynamics, which provides new insights into crop management and breeding strategies for sustainable Fe improvement in agricultural production.

The bioavailability of iron is limited by the solubility of Fe(III) at circumneutral pH. In the High Nutrient-Low Chlorophyll (HNLC) zones of the ocean, the natural or anthropogenic addition of iron stimulates primary productivity and consumes carbon dioxide. As a result, iron fertilization has been proposed to mitigate anthropogenic carbon emissions and lower global temperatures. The natural sources of iron to the ocean are not fully constrained and include eolian depositions as well as inputs from continental shelf sediments, rivers, hydrothermal vents, and icebergs. Regardless of their source, the effectiveness of iron additions in promoting carbon fixation depends on the presence of organic ligands either natural or produced by microorganisms that stabilize or solubilize Fe(III) at neutral pH. For example, siderophores are well known to be expressed extracellularly by prokaryotes in the photic zones of the oceans to increase the bioavailability of iron. In this dissertation, the production of iron nanoparticles is demonstrated in vent fluids from the 90 North hydrothermal system. These iron nanoparticles may either catalyze the oxidation of sulfide to thiosulfate and produce a potential electron acceptor for microbial respiration or provide a source of iron that stimulates primary production at great distances from the hydrothermal vents. In addition, dissolved iron under the form of soluble organic-Fe(III) complexes is demonstrated to constitute a significant source of iron in estuarine sediments that receive large amounts of particulate iron from flocculation and precipitation at the salinity transition of this estuary. A novel competitive ligand equilibration absorptive cathodic stripping voltammetry (CLE-ACSV) technique reveals that the speciation of iron changes from largely colloidal or particulate in the upper estuary to truly dissolved organic-Fe(III) in the lower estuary. It is also demonstrated that organic-Fe(III) complexes are produced far below the sediment-water interface, suggesting that dissimilatory iron-reducing bacteria may play an important role in their production. These complexes then diffuse across the sediment-water interface and provide a significant source of iron to the continental shelf. The mechanism of reduction of iron oxides by iron-reducing bacteria is not fully understood and presents a unique physiological problem for the organism, as the terminal reductase has to transfer electrons to a solid electron acceptor. In this dissertation, it is demonstrated for the first time using random mutagenesis that the respiration of solid Fe(III) oxides by Shewanella oneidensis, a model iron-reducing prokaryote, first proceeds through a non-reductive dissolution step involving organic ligands that are released extracellularly by the cells. These soluble complexes are then reduced by the organism to produce Fe(II) and recycle the ligand for additional solubilization. Incubations with deletion mutants of the proteins involved in the respiration of Fe(III) revealed that the type-II secretion system, which translocates proteins on the outer membrane of gram-negative bacteria, is involved in the production of organic-Fe(III) complexes by secreting an endogenous iron-solubilizing ligand or a protein involved in the biosynthesis of this ligand on the outer membrane. In addition, periplasmic decaheme cytochromes produced by Shewanella appear to be involved in the mechanism of production of the endogenous organic ligand either directly or through a sensing mechanism that controls its production. In turn, two decaheme cytochromes positioned on the outer-membrane and hypothesized to be involved in the electron transfer to the mineral surface do not appear to be involved in the solubilization mechanism, suggesting either that the cells regulate the ligand production via periplasmic sensing systems or that these cytochromes are not involved in the solubilization mechanism. Altogether this research shows the production of organic-Fe(III) complexes in sediments generates a significant flux of dissolved iron to support primary production in continental shelf waters and that these complexes may be partly produced by iron-reducing bacteria. Indeed, experiments with a model organism demonstrate dissimilatory iron reducing bacteria produce endogenous organic ligands with high iron-binding constants to non-reductively solubilize iron oxides during the anaerobic respiration of iron oxides. The organic ligand is apparently recycled several times to minimize the energy cost associated with its biosynthesis. These findings demonstrate that the solubilization of iron oxides by organic ligands may be an important, yet underappreciated process in aquatic systems.

Varved (annually laminated) sediments are of great interest for inference of past environmental conditions, as they provide dated records with high time resolution. After deposition, the sediment varves are affected by diagenesis; i.e., chemical, physical and biological changes that occur within the sediment. An important premise when reconstructing past environmental conditions using lake sediments is that the signal of interest is preserved in the sediment. In this thesis I have used a unique collection of ten stored freeze cores of varved lake sediment from Nylandssjön in northern Sweden, collected from 1979 to 2007. The suite of cores made it possible to follow long-term (up to 27 years) changes in iron (Fe), sulfur (S), carbon (C), nitrogen (N), δ13C and δ15N in the sediment caused by processes that occur in the lake bottom as the sediment ages. The sediment geochemistry and resulting changes were followed in years for which there are surface varves in the core series. Fe and S concentrations analyzed by X-ray fluorescence spectroscopy showed no diagenetic front in the sediment and the data do not suggest a substantial vertical transport of Fe and S in the sediment. A model based on thermodynamic, limnological, and sediment data from the lake, showed that there are pe (redox) ranges within which either FeS (reduced specie) or Fe(OH)3/FeOOH oxidized species) is the only solid phase present and there are pe ranges within which the two solid phases co-exist. This supports the hypothesis that blackish and grey-brownish Fe-layers that occur in the varves were formed at the time of deposition. C and N analyzed with an elemental analyzer showed that within the first five years after deposition the C concentration of the sediment decreased by 20% and N by 30%, and after 27 yr in the sediment, there was a 23% loss of C and 35% loss of N. The C:N ratio increased with increasing age of the sediment; from ~ 10 in the surface varves to ~12 after 27 years of aging. δ13C and δ15N analyzed on a mass spectrometer showed that δ13C increased by 0.4-1.5‰ units during the first five years, after that only minor fluctuations in δ13C were recorded. Another pattern was seen for δ15N, with a gradual decrease of 0.3-0.7‰ units over the entire 27-year-period. The diagenetic changes in the stable isotope values that occur in Nylandssjön are minor, but they are of about the same magnitude as the variation in the isotopic signal in the varves deposited between 1950-2006. My results show that diagenesis does not change the visual appearance of the varves, except for varve thickness; the varves get thinner as the sediment ages. As the color of Fe in the varves likely reflects the environmental conditions at the time of deposition this creates possibilities for deciphering high-temporal-resolution information of past hypolimnetic oxygen conditions from varves. My findings on C, N, δ13C and δ15N will have implications for interpretations of paleolimnological data. The diagenetic effects should be carefully taken into consideration when C, N, δ13C and δ15N in sediment cores are used to study organic matter sources or paleoproductivity, in particular when dealing with relatively small and recent changes. In addition to the significance of diagenetic effects on sediment parameters, a comparison of the varves in Nylandssjön and the adjacent lake Koltjärnen, and the two deep basins of Nylandssjön show that subtle features in the lakes and their catchments affect the appearance of the varves, which make interpretation of varves complicated.

No description available.