Soil contamination with arsenic (As), a carcinogen, is a global problem that stems from irrigation with arsenic-contaminated water, use of arsenical pesticides, fossil fuel combustion, and industrial processes including mining, smelting, and glass production. Plant-based removal of arsenic from soil, or phytoextraction, with the fern Pteris vittata L. is an emerging in situ technology potentially suitable for moderately contaminated soils. While theoretically promising, field application of phytoextraction with P. vittata faces limitations due to variable and slow arsenic uptake rates and long remediation times. Fertilization with nitrogen or phosphorus, and inoculation with mycorrhizal fungi, have been shown to increase arsenic uptake rates under simplified hydroponic or pot experiment conditions. It is unclear whether those findings might apply to field conditions where plant roots are not confined to a limited volume of growth media and where soil texture and arsenic concentrations could be heterogeneously distributed.

In my dissertation I determined the effects of soil biogeochemical and physical characteristics, including 1) soil fertilization or inoculation with mycorrhizal fungus Funneliformis mosseae, 2) soil texture, and 3) soil arsenic concentration, on arsenic phytoextraction with P. vittata using a multi-scale approach. To test the feasibility of phytoextraction in fine-textured soils, I conducted a large-scale, 4-year field study at a prospective urban agriculture site (Berkeley, CA; 16-361 mg As/kg) working with community collaborators. To test whether leaching could limit the practical application of phytoextraction with P. vittata, I conducted a 1-year, high spatiotemporal resolution field study at a California superfund site (Richmond, CA; 25-114 mg As/kg). To determine mechanisms of arsenic mobilization and transport in soil during phytoextraction, I conducted a 0.4-year mesocosm study using novel unsaturated soil columns planted with P. vittata.

Across all studies, I found that P. vittata was best-suited to phytoextract arsenic from nutrient-poor soils. Nutrient application had either no, or a negative, effect on arsenic uptake rates in P. vittata. In the 4-year field and mesocosm studies, uptake rates were negatively correlated with percentage clay, which was associated with increased nutrient content. In the 1-year field and mesocosm studies, I showed that arsenic was mobilized for uptake in P. vittata through ion exchange processes also known to mobilize phosphorus, and therefore, according to the phosphorus starvation framework, arsenic uptake could be a byproduct of nutrient scavenging processes most active in nutrient-poor soils. My results suggest that mycorrhizal fungi could increase arsenic tolerance through mechanisms other than nutrient transport. In the 1-year field study, inoculation with F. mosseae led to higher fern biomass, slightly higher uptake rates and significantly lower remediation times.

P. vittata removed a mean of 3.6% of initial soil arsenic in the 1-year field study. Across the 1- and 4-year field studies, P. vittata arsenic removal rates ranged from 0.02±NA to 28.9±11.1 kg As/ha/yr, leading to highly variable and long remediation time estimates (12 to >1000 years). In the 1-year field study, soil arsenic concentrations were positively correlated with arsenic uptake rates but did not affect remediation times, indicating that a given soil was remediated equally efficiently regardless of arsenic concentration. Across the 1- and 4-year field studies, changes in soil arsenic concentrations were not consistent with fern arsenic accumulation and indicated complex cycling of arsenic during phytoextraction. In the 4-year field study, surface soil arsenic concentrations significantly increased in the coarse-textured soil, where greater fern growth and arsenic accumulation was observed, suggesting phytoenrichment of arsenic in surface soils over longer (>1 year) time periods. However, in the 4-year field study in the fine-textured soil, where fern growth was lower and mortality higher, arsenic concentrations were greater in the lower than surface depth interval, suggesting arsenic leaching. Furthermore, in the 1-year field study, soil arsenic concentrations significantly decreased, with a greater decrease in the lower (10-20 cm) than surface depth interval (0-10 cm).

I quantified the first (to my knowledge) mass balance equating P. vittata arsenic uptake to significant decreases in soil arsenic, and found that arsenic uptake in P. vittata could explain only 38.5% of total arsenic depletion from soil in the 1-year field study. This discrepancy in the arsenic mass balance suggests arsenic leached in the 1-year field study, a finding I confirmed under mesocosm conditions. In the 1-year field and mesocosm studies, I showed that arsenic could leach as a result of rhizosphere processes mobilizing arsenic, processes which appeared primarily responsible for arsenic uptake in P. vittata. In both studies I found arsenic chemistry in the rhizosphere was distinct from in bulk soil, suggesting the rhizosphere was a unique reactive zone for arsenic mobilization. Furthermore, I found under mesocosm conditions that arsenic transported from bulk soil to the fern via transpiration flux of porewater accounted for <30% of arsenic content in P. vittata, indicating most uptake comes directly from rhizosphere soil. My results suggest the geochemical processes promoting arsenic mobilization in the rhizosphere could lead to arsenic leaching from both rhizosphere soil and bulk soil in proximity to, and below, the root zone. Indeed, arsenic budgets in the mesocosm study showed that arsenic leached at higher concentrations in the presence compared to absence of P. vittata. In the mesocosm study, smaller biomass, which appeared to be the metabolic cost of tolerating highly phytoavailable arsenic, led to greater leaching.

Overall, nutrient-rich soils, presence of clay, and arsenic leaching limited arsenic phytoextraction. Across all studies, I showed that over short time periods in simple systems, arsenic accumulation in P. vittata exceeds loss to leaching, but that over time periods of 1 to 4 years, leaching can exceed fern arsenic accumulation, and phytoenrichment of arsenic from aboveground biomass back to surface soils can increase surface soil concentrations. My work emphasizes the importance of rhizosphere processes to bulk geochemical cycles.

Natural and human impacts on geochemical redox cycling and biodiversity in estuaries have long been a global concern. In estuarine systems, sulfur (S) is a macroelement of great environmental importance. The production and oxidation of hydrogen sulfide (H2S) are highly impacted by biogeochemical and physical conditions, including redox conditions and pH. For decades, hydrogen sulfide (H2S) has been recognized as a major contaminant in estuarine systems due to its direct (toxicity) and indirect (oxidative) effects on aquatic and sediment life. Mass mortality events of fish and migratory birds have occurred in various coastal ecosystems, including bar-built estuaries, which serve as major ecological habitats and as water-purifying marshlands. In this dissertation, I develop an integrated and comprehensive understanding of the geochemical and biological transformations involved in the sulfur redox cycling at the interface of the hydrosphere and pedosphere in a northern California bar-built estuary (Pescadero Estuary, CA) and their consequences on water quality. Fish kills have been more regular and severe at Pescadero than at other nearby California bar-built systems. Across scientific disciplines and spatial and temporal scales, I begin by illustrating the temporal evolution in geochemical conditions in water and sediment from closed to open state to accentuate the decline in water conditions as the estuary opens. I then examine the major anaerobic respiration pathways controlling the biogeochemical cycling of sulfur and its effects on iron (Fe) cycling and pH. Finally, using flow-through reactor experiments and slurry incubations, I investigate the biogeochemical mechanisms that control the production, precipitation, and re-oxidation of hydrogen sulfide in water and sediment.

Common in Mediterranean climates (e.g. United States, South Africa, Australia, Europe), intermittent estuaries have received little research attention, which lacks in information on the geochemistry of the systems. In California, bar-built estuaries represent about 75% of over 400 estuaries along the Pacific coastline and function as critical refuges to migratory and endangered fish communities, including federally-threatened steelhead trout (Oncorhynchus mykiss). An established watershed spanning centuries of human use, the bar-built Pescadero Estuary has, however, been afflicted by near-annual fish mortality events of steelhead trout since 1995, occurring with the natural or anthropogenic opening of the sandbar barrier. In Chapter 1, I tracked the temporal and spatial evolution of water and sediment geochemical conditions from closed to open state to highlight the decline in water conditions between states, specifically acidification. This extensive sampling campaign was feasible for this relatively small system and illustrated that the northern tributary, Pescadero Creek, showed a significant departure in geochemical conditions from the rest of the Estuary; this implied that it may be considerably less susceptible to fish die-offs than the rest of the Pescadero Estuary.

Using this large-scale interpretation of the Pescadero Estuary, I chose four contrasting study to investigate in more details biogeochemical redox cycling of sulfur and iron in sediment during the closed and open states. The speciation and cycling of sulfur are largely driven by microbial activity and redox conditions. The analysis of Pescadero Estuary pore water profiles confirmed that microbial sulfate reduction to hydrogen sulfide is the dominant anaerobic respiration pathway in both the closed and open states. Moreover, the absence of nitrate and presence of reduced ferrous iron confirmed suboxic, reducing conditions in water and the steady production of acid-volatile sulfides (AVS) and iron sulfides in sediment. Additionally, I observed that iron reduction and sulfate reduction occur concomitantly. In Chapter 3, I corroborated that sulfate reductive processes predominate in the Pescadero Estuary, with greater rates in the closed state than in the open state and also in fine-grained sediments than in coarse-grained sediments. Despite higher values than the EPA-defined criterion for aquatic life, the low concentrations of aqueous hydrogen sulfide imply that it cannot solely cause fish deaths. The majority of aqueous sulfide precipitates as metal sulfides in sediment, who could indirectly be implicated in fish die-offs in the transition from closed to open state upon re-oxidation.

The coupled interactions between physical state, sediment conditions, water quality, and overall estuarine health are complex. Linked to climatic conditions and water inflows from ocean and freshwater, the transitional period from closed to open state is characterized by sediment resuspension and mobilization of sediment metal sulfides into the water column where they can be oxidized. In Chapter 4, I demonstrated the oxidative effects of Pescadero Estuary sediments on water conditions using slurry incubation resuspension experiments. I confirmed that aqueous hydrogen sulfide concentrations were low and oxidized quickly (<1 day) and therefore cannot be responsible for fish kills, consistent with the results from Chapter 3. In contrast, the oxidation of sediment AVS was slower, and resulted in their complete removal in six days, with large contents of sulfur released from sediment to water. The oxidation of AVS leads to severe acidification and release of metals (iron, manganese, and zinc) to water. The aqueous metal concentrations reached were greater than the EPA-defined maximum criteria for aquatic life, indicating a potential link to poor fish health.

The integration of scientific knowledge across spatial, environmental, and ecological scales is rarely attempted, thus limiting our mechanistic understanding of sulfur cycling and the causal reasons for mortality events in bar-built estuaries globally. The role of sediment and its impacts on ecosystem health, water quality, and aquatic life due to natural and anthropogenic causes is particularly important. This work is the first to examine the natural, direct and indirect effects of hydrogen sulfide at the interface of water and sediment and across spatial and temporal scales in a bar-built estuary. It is also the first to undertake an extensive sampling campaign to pinpoint the temporal evolution of geochemical conditions. As a comprehensive examination of a complex, environmental problem, this study represents an important advancement in the fields of water, soil, and estuarine science. The management and remediation of intermittent systems depends on our ability to predict estuarine conditions, which will be also be used for similar estuaries along the California coast and to meet policy criteria for water quality. Further development of sulfur cycling across scientific disciplines, landscape types, and coastal environments will be achievable to minimize the likelihood of fish mortality events.

The Salton Sea in California was formed between 1905-1907 by an accident that diverted Colorado River water to the Salton Sea Basin of the Colorado desert. Since 1924 the Salton Sea serves as an agricultural drainage reservoir maintained by agricultural and municipal wastewater inputs from the Coachella and Imperial Valleys in California and the Mexicali Valley in Mexico. Today, the Salton Sea is California's largest lake by area (975 km2) and constitutes a vital habitat for more than a million birds belonging to more than 400 species, including migratory and endangered populations. The Salton Sea, however, has been called an “ecological time bomb” given the threat that the convergence of selenium accumulation, chemical pollution, water diversion and climate change poses to this unique environment.

Selenium (Se) is considered an “essential toxin” due to its role as both an essential nutrient and an environmental contaminant. Selenium contamination is a concern in important areas of the United States, Canada, Mexico, Egypt and Israel where mining, agriculture and the extraction and refinement of fossil fuels and metals lead to selenium release from seleniferous parent rock material and selenium bioaccumulation in wildlife.

In aquatic ecosystems, selenium bioaccumulation is preceded by the accumulation of selenium in sediment which is driven by sorption and microbial activity, more specifically, the assimilatory and dissimilatory reduction of water-soluble selenium oxyanions. For the Salton Sea it remains unclear whether the sorptive and reductive capacity of sediments will suffice to prevent dissolved selenium concentrations in water from increasing in the future.

In order to characterize the transfer of selenium from water to underlying sediments in the Salton Sea, in this dissertation I describe the spatial variability in sediment parameters controlling selenate reduction rates across seven geographical locations and four depth intervals. I identify organic carbon content in sediment as an important driver of selenium accumulation in Salton Sea littoral sediment due to its dual nature as a sorbant for selenium oxyanions and as a source of reducing power for sediment microbial communities capable of selenate reduction. In the the first chapter, I quantify organic carbon content, selenate reducer abundance, selenium content and potential selenate reduction rates using sediment slurries in sediment collected from seven Salton Sea littoral locations. I show a broad diversity of sediment characteristics and the effect of sediment organic carbon content on selenate reduction potential.

In the second chapter, I show a range of Km and Rmax values for selenate and selenate reduction, respectively, comparable to that obtained in sediment collected from eleven geographical locations in the states of California and Nevada. Km values for selenate in evaluated sediment are well above ambient selenate concentrations and therefore microbial communities capable of selenate reduction operate well below their selenate reduction potential. I also show unexpectedly high selenate sorption which, under present conditions, contributes more than microbial activity to selenium retention in sediment.

In the third chapter, I use sediment slurries and a microbial consortium recovered from Salton Sea littoral sediment to suggest that nitrate reducers play an important role in selenium accumulation in the Salton Sea. I discuss this data in the context of our current knowledge regarding the microbial pathways of selenate reduction and the thermodynamic constraints associated with selenate respiration and microbial biomass synthesis.

Bacterial surfaces can be used in engineered systems through the implementation of bioreactors as unconventional means of extracting critical metals. This dissertation discusses a genetically modified gram-negative bacterium, dLBTx8 induced Escherichia coli, which possesses lanthanide binding tag peptides that chelate and preferentially adsorb rare earth elements over other co-existing metals. A thermodynamic surface complexation model was first built to compare the cell surface terbium binding mechanisms of wild type and dLBTx8 engineered E. coli (Ch. 2). This surface complexation model was then expanded upon to include adsorption of yttrium and thirteen lanthanide elements (Ch. 3). The engineered dLBTx8 E. coli cells were immobilized in a non-sorbing polyethylene glycol diacrylate (PEGDA) polymer and packed into fixed-bed columns to demonstrate proof-of-principle bioreactor designs. A one-dimensional reactive transport model incorporating advective inter-bead and diffusive intra-bead transport of lanthanides was developed to account for the complex competitive adsorption processes taking place within the dLBTx8 E. coli packed fixed-bed column. After careful calibration and testing of the reactive transport model, predictions were made to optimize separation of valuable rare earths, exemplified by europium vs. lanthanum separation. This dissertation demonstrates the power of surface complexation and reactive transport modeling to allow for future engineering designs that can improve the efficacy of rare earth element bio-extraction and separation from geothermal fluid and mining leachate feedstocks.Bacterial surfaces can also play an important role in soils, surface water, and subsurface geologic systems, where the cell surface-based ligands can adsorb various metals. Due to the reactive nature of their cell surfaces, bacteria can influence fate, transport, and mobility of naturally occurring and anthropogenically introduced metals in soils. While many scientists have investigated the adsorption of divalent metals, such as lead and copper, onto bacterial surfaces found in soils and sediments, a knowledge gap currently exists in understanding how trivalent lanthanides impact these dynamic subsurface transport processes. In general, soil bacterial surfaces have been shown to have particularly strong electrostatic interactions with rare earths, implying that these trivalent metals can act as important controls over the transport of divalent metals. In this dissertation, a gram-positive soil bacterium, Arthrobacter nicotianae, has been shown to adsorb lanthanides through multiple different surface complexation mechanisms, including phosphodiester, phosphoryl, carboxyl, and carbonyl-based amide binding (Ch. 4). These results, supported through attenuated total reflectance Fourier transform infrared spectroscopy measurements (ATR-FTIR), are qualitatively corroborated by thermodynamic modeling of the bacterial cell wall. Notably, the modeling results suggest the relatively high affinities imposed by each of these site types, particularly through phosphate and amide monodentate adsorption. This work contributes to the currently existing knowledge gap whereby soil transport of divalent metals may significantly be affected by the presence of even low concentrations of trivalent rare earth elements.