abstract: Molybdenum (Mo) is a key trace nutrient for biological assimilation of nitrogen, either as nitrogen gas (N2) or nitrate (NO3-). Although Mo is the most abundant metal in seawater (105 nM), its concentration is low (<5 nM) in most freshwaters today, and it was scarce in the ocean before 600 million years ago. The use of Mo for nitrogen assimilation can be understood in terms of the changing Mo availability through time; for instance, the higher Mo content of eukaryotic vs. prokaryotic nitrate reductase may have stalled proliferation of eukaryotes in low-Mo Proterozoic oceans. Field and laboratory experiments were performed to study Mo requirements for NO3- assimilation and N2 fixation, respectively. Molybdenum-nitrate addition experiments at Castle Lake, California revealed interannual and depth variability in plankton community response, perhaps resulting from differences in species composition and/or ammonium availability. Furthermore, lake sediments were elevated in Mo compared to soils and bedrock in the watershed. Box modeling suggested that the largest source of Mo to the lake was particulate matter from the watershed. Month-long laboratory experiments with heterocystous cyanobacteria (HC) showed that <1 nM Mo led to low N2 fixation rates, while 10 nM Mo was sufficient for optimal rates. At 1500 nM Mo, freshwater HC hyperaccumulated Mo intercellularly, whereas coastal HC did not. These differences in storage capacity were likely due to the presence in freshwater HC of the small molybdate-binding protein, Mop, and its absence in coastal and marine cyanobacterial species. Expression of the mop gene was regulated by Mo availability in the freshwater HC species Nostoc sp. PCC 7120. Under low Mo (<1 nM) conditions, mop gene expression was up-regulated compared to higher Mo (150 and 3000 nM) treatments, but the subunit composition of the Mop protein changed, suggesting that Mop does not bind Mo in the same manner at <1 nM Mo that it can at higher Mo concentrations. These findings support a role for Mop as a Mo storage protein in HC and suggest that freshwater HC control Mo cellular homeostasis at the post-translational level. Mop's widespread distribution in prokaryotes lends support to the theory that it may be an ancient protein inherited from low-Mo Precambrian oceans. / Dissertation/Thesis / Ph.D. Geological Sciences 2011

Humans have dramatically increased the amount of reactive nitrogen cycling through the biosphere. In coastal systems, excess nitrogen can lead to negative impacts. Thus, it is crucial to understand how nitrogen is cycled within, and eventually removed from, marine systems and the variables that regulate these processes. Sediment denitrification (the microbial conversion of nitrate (NO3^-) to dinitrogen (N2) gas) and water column nitrification (the two step oxidation of ammonium (NH4^+) to nitrite (NO2^-) and then nitrate (NO3^-)) rates were quantified along an in situ gradient of environmental conditions from an estuary to the continental shelf off Rhode Island, USA. Sediment net denitrification rates were directly measured over multiple seasonal cycles using the N2/Ar technique. Denitrification rates ranged from 20-75 μmol m^-2 hr^-1 (mean 44±4), indicating that this process removes ~5% of total reactive nitrogen entering the North Atlantic shelf region per year. Based on model results, these rates also represented a three-fold decrease in sediment nitrogen removal in New England continental shelf sediments over the past century. A literature review of marine water column nitrification observations were compiled to evaluate how ammonium, nitrite, and total oxidation rates vary worldwide. Rates of ammonium, nitrite, and total oxidation differed among estuary, continental shelf, and open ocean environments (p<0.05). This review highlights that as we continue to study marine "nitrification," it is necessary to consider both individual oxidation processes and environment type. Water column ammonium and nitrite oxidation rates were measured using stable isotope tracers off Rhode Island. At all study sites, nitrite oxidation rates (0-99 nM d^-1) outpaced ammonium oxidation rates (0-20 nM d^-1). These oxidation processes responded in dissimilar ways to in situ water column conditions (depth, salinity, dissolved oxygen, and pH), and these relationships varied with location. Nitrous oxide (N2O) production rates up to 10 times higher than ammonium oxidation indicated that ammonium oxidation may be underestimated if this byproduct is not measured. For the first time, the link between sediment metabolism and water column nitrification was also examined, and the results highlight the importance of benthic-pelagic coupling as controlling factor of water column ammonium and nitrite oxidation. / 2019-04-30T00:00:00Z

Mean winter air temperatures have risen by 2.5˚C over the last 50 years in the northeastern U.S., reducing mean annual winter snowpack depth by 26 cm and the duration of winter snow cover by four days per decade. Because snow cover insulates soil from below-freezing air temperatures, continued declines in snowpack depth are projected to be accompanied by colder winter soil temperatures and more frequent soil freeze-thaw events. Soil bacteria and fungi will play a significant role in the forest ecosystem response to snowpack loss because they are the primary agents that carry out soil organic matter decomposition and soil nutrient cycling. Additionally, the effect of winter snowpack decline on soil bacterial and fungal communities may act indirectly via winter climate change effects on plant roots. The objectives of my dissertation research were to first determine the effect that reductions in winter snow cover has on microbial exoenzyme activity, microbial respiration, net nitrogen (N) mineralization, and net nitrification rates in two mixed-hardwood forests (Harvard Forest, MA and Hubbard Brook Experimental Forest, NH). Additionally, I sought to determine the relative role that abiotic factors (i.e., winter snow cover or soil frost) versus biotic factors (i.e., altered root-microbe interactions) contribute to overall changes in soil biogeochemical processes as winter snow cover declines. I found that winter snow depth and duration are related positively to microbial exoenzyme activity and microbial respiration following snowmelt in spring, but this relationship is transient and attenuates into the growing season. By contrast, soil freeze-thaw events during winter result in persistent declines in microbial oxidative enzyme activity that are not compensated for by warming soils during the growing season. Together, these results suggest that loss of winter snow cover will result in lower rates of nutrient cycling in northeastern U.S. hardwood forests. Tree roots interact with winter snow depth to affect net mineralization and nitrification rates, as well as bacterial and fungal community composition. Thus, winter climate change portends a reorganization of root-microbe interactions with important consequences for soil biogeochemical cycling in mixed hardwood forests of the northeastern U.S.

Recent field observations suggest that the radiative forcing of aerosol and clouds in the Arctic may be seasonally regulated by the oceanic emissions of the climatically-important biogenic trace gas dimethylsulfide (DMS). However, the validity of the proposed argument is challenged by the limited spatio-temporal coverage of these earlier studies in this difficult-to-access region. In particular, little is known about the pan-Arctic distribution of the oceanic DMS emissions, its temporal variability, and the impacts of sea-ice biogeochemistry on these emissions. In this dissertation, I investigated these unexplored subjects through numerical modelling. Using a one-dimensional (1-D) column modelling framework, I developed a coupled sea ice-ocean biogeochemical model and assessed the impacts of bottom-ice algae ecosystems on the underlying pelagic ecosystems and the associated production and emissions of DMS. The model was calibrated by time-series measurements of snow and melt-pond depth, ice thickness, bottom-ice and under-ice concentrations of chlorophyll-a and dimethylsulfoniopropionate (DMSP), and under-ice irradiance obtained on the first-year landfast sea ice in Resolute Passage during May-June of 2010. Many of the model parameters for the DMSP and DMS production and removal processes were derived from recent field measurements in the Arctic, which is advantageous over the previous Arctic-focused DMS model studies as their model parameters were based on the measurements in extra-polar regions. The impacts of sea-ice biogeochemistry on the DMS production in the underlying water column and its potential emissions into the overlying atmosphere were quantified through sensitivity experiments. To extend the study domain to the pan-Arctic, I implemented the sea-ice ecosystem and the coupled sea ice-pelagic DMS cycling components of the 1-D column model into a three-dimensional (3-D) regional modelling framework. A multi-decadal model simulation was performed over the period 1969-2015 using realistic atmospheric forcing and lateral boundary conditions. The results of the simulation were evaluated by direct comparisons with available data products and reported values based on field and satellite measurements and other model simulations. The decline of Arctic sea ice was successfully simulated by the model. The magnitude of the pan-Arctic sea-ice and pelagic annual primary production and their general spatial patterns were comparable to other model studies. The mean seasonal cycle and the spatial distribution of the model-based surface seawater DMS climatology within the pan-Arctic showed some similarities with in situ measurement- and satellite-based climatologies. However, at the same time, the comparison of the DMS climatologies was challenged by the bias in the measurement-based climatology, emphasizing the need to update this data product, which was created almost a decade ago, by incorporating data acquired during the recent field campaigns. The analysis of the modelled fluxes of DMS at the ice-sea and sea-air interfaces revealed different responses to the accelerated decline of sea ice over the recent decades (1996-2015). There was no trend in the pan-Arctic ice-to-sea DMS flux due to the counteracting effect of vertical thinning and horizontal shrinking of sea ice that drove ice algal production. In contrast, the pan-Arctic sea-to-air DMS flux showed a consistent increase (about 40 % over the last two decades) driven by the reduction of sea ice cover that promoted outgassing and biological productivity. This finding suggests that the climate warming in the Arctic causes an increase in DMS emissions, and encourages further exploration of the biological climate regulation in the Arctic. / Graduate

abstract: Humans have dramatically increased phosphorus (P) availability in terrestrial and aquatic ecosystems. As P is often a limiting nutrient of primary production, changes in its availability can have dramatic effects on ecosystem processes. I examined the effects of calcium carbonate (CaCO3) deposition, which can lower P concentrations via coprecipitation of phosphate, on P availability in two systems: streams in the Huachuca Mountains, Arizona, and a stream, Río Mesquites, in Cuatro Ciénegas, México. Calcium carbonate forms as travertine in the former and within the microbialites of the latter. Despite these differences, CaCO3 deposition led to lowered P availability in both systems. By analyzing a three-year dataset of water chemistry from the Huachuca Mountain streams, I determined that P concentrations were negatively related to CaCO3 deposition rates. I also discovered that CaCO3 was positively correlated with nitrogen concentrations, suggesting that the stoichiometric effect of CaCO3 deposition on nutrient availability is due not only to coprecipitation of phosphate, but also to P-related constraints on biotic nitrogen uptake. Building from these observations, bioassays of nutrient limitation of periphyton growth suggest that P limitation is more prevalent in streams with active CaCO3 deposition than those without. Furthermore, when I experimentally reduced rates of CaCO3 deposition within one of the streams by partial light-exclusion, areal P uptake lengths decreased, periphyton P content and growth increased, and periphyton nutrient limitation by P decreased. In Río Mesquites, CaCO3 deposition was also associated with P limitation of microbial growth. There, I investigated the consequences of reductions in CaCO3 deposition with several methods. Calcium removal led to increased concentrations of P in the microbial biomass while light reductions decreased microbial biomass and chemical inhibition had no effect. These results suggest that CaCO3 deposition in microbialites does limit biological uptake of P, that photoautotrophs play an important role in nutrient acquisition, and, combined with other experimental observations, that sulfate reduction may support CaCO3 deposition in the microbialite communities of Río Mesquites. Overall, my results suggest that the effects of CaCO3 deposition on P availability are general and this process should be considered when managing nutrient flows across aquatic ecosystems. / Dissertation/Thesis / Doctoral Dissertation Biology 2015

abstract: This dissertation addresses the role of kinship and residential mobility during the transition from Final Neolithic to Early Bronze Age (ca. 3500 – 2500 BC) in Attica, Greece. It examines descent systems, ancestor formation, and the interplay between biological, social, and spatial structure in mortuary practices. It also evaluates the nature and degree of residential mobility and its potential role in the formation and maintenance of social networks. Archaeological hypotheses on the kin-based structure of formal cemeteries, the familial use of collective tombs, marriage practices and mate exchange, and relocation were tested focusing on the Early Helladic cemetery of Tsepi at Marathon. Tsepi constitutes the earliest formally organized cemetery on the Greek mainland and it has also contributed to enduring debates over the nature of the interaction between the eastern Attic coast and the central Aegean islands. This study integrates osteological, biogeochemical, and archaeological data. Inherited dental and cranial features were used to examine biological relatedness and postmarital residence (biodistance analysis). Biochemical analysis of archaeological and modern samples was conducted to examine the geographic origins of the individuals buried in the cemetery and reconstruct mobility patterns. Osteological and biogeochemical data were interpreted in conjunction with archaeological and ethnographic/ethnohistoric data. The results generally supported a relationship between spatial organization and biological relatedness based on phenotypic similarity at Tsepi. Postmarital residence analysis showed exogamous practices and tentatively supported higher male than female mobility. This practice, along with dietary inferences, could also be suggestive of maritime activities. Biogeochemical analysis showed a local character for the cemetery sample (96%). The common provenance of the three non-local individuals might reflect a link between Tsepi and a single locale. Burial location was not determined by provenance or solely by biological relatedness. Overall, the results point towards more nuanced reconstructions of mobility in prehistoric Aegean and suggest that burial location depended on a complex set of inter-individual relationships and collective identities. The contextualized bioarchaeological approach applied in this study added to the anthropological investigations of social practices such as kin relations (e.g., biological, marital, social kinship) and residential relocation as diachronic mechanisms of integration, adaptation, or differentiation. / Dissertation/Thesis / Doctoral Dissertation Anthropology 2015

abstract: Many acidic hot springs in Yellowstone National Park support microbial iron oxidation, reduction, or microbial iron redox cycling (MIRC), as determined by microcosm rate experiments. Microbial dissimilatory iron reduction (DIR) was detected in numerous systems with a pH < 4. Rates of DIR are influenced by the availability of ferric minerals and organic carbon. Microbial iron oxidation (MIO) was detected from pH 2 – 5.5. In systems with abundant Fe (II), dissolved oxygen controls the presence of MIO. Rates generally increase with increased Fe(II) concentrations, but rate constants are not significantly altered by additions of Fe(II). MIRC was detected in systems with abundant ferric mineral deposition. The rates of microbial and abiological iron oxidation were determined in a variety of cold (T= 9-12°C), circumneutral (pH = 5.5-9) environments in the Swiss Alps. Rates of MIO were measured in systems up to a pH of 7.4; only abiotic processes were detected at higher pH values. Iron oxidizing bacteria (FeOB) were responsible for 39-89% of the net oxidation rate at locations where biological iron oxidation was detected. Members of putative iron oxidizing genera, especially Gallionella, are abundant in systems where MIO was measured. Speciation calculations reveal that ferrous iron typically exists as FeCO30, FeHCO3+, FeSO40 or Fe2+ in these systems. The presence of ferrous (bi)carbonate species appear to increase abiotic iron oxidation rates relative to locations without significant concentrations. This approach, integrating geochemistry, rates, and community composition, reveals biogeochemical conditions that permit MIO, and locations where the abiotic rate is too fast for the biotic process to compete. For a reaction to provide habitability for microbes in a given environment, it must energy yield and this energy must dissipate slowly enough to remain bioavailable. Thermodynamic boundaries exist at conditions where reactions do not yield energy, and can be quantified by calculations of chemical energy. Likewise, kinetic boundaries exist at conditions where the abiotic reaction rate is so fast that reactants are not bioavailable; this boundary can be quantified by measurements biological and abiological rates. The first habitability maps were drawn, using iron oxidation as an example, by quantifying these boundaries in geochemical space. / Dissertation/Thesis / Doctoral Dissertation Geological Sciences 2017

abstract: In many natural systems aqueous geochemical conditions dictate the reaction pathways of organic compounds. Geologic settings that span wide ranges in temperature, pressure, and composition vastly alter relative reaction rates and resulting organic abundances. The dependence of organic reactions on these variables contributes to planetary-scale nutrient cycling, and suggests that relative abundances of organic compounds can reveal information about inaccessible geologic environments, whether from the terrestrial subsurface, remote planetary settings, or even the distant past (if organic abundances are well preserved). Despite their relevance to planetary modeling and exploration, organic reactions remain poorly characterized under geochemically relevant conditions, especially in terms of their reaction kinetics, mechanisms, and equilibria. In order to better understand organic transformations in natural systems, the reactivities of oxygen- and nitrogen-bearing organic functional groups were investigated under experimental hydrothermal conditions, at 250°C and 40 bar. The model compounds benzylamine and α-methylbenzylamine were used as analogs to environmentally relevant amines, ultimately elucidating two dominant deamination mechanisms for benzylamine, SN1 and SN2, and a single SN1 mechanism for deamination of α-methylbenzylamine. The presence of unimolecular and bimolecular mechanisms has implications for temperature dependent kinetics, indicating that Arrhenius rate extrapolation is currently unreliable for deamination. Hydrothermal experiments with benzyl alcohol, benzylamine, dibenzylamine, or tribenzylamine as the starting material indicate that substitution reactions between these compounds (and others) are reversible and approach metastable equilibrium after 72 hours. These findings suggest that relative ratios of organic compounds capable of substitution reactions could be targeted as tracers of inaccessible geochemical conditions. Metastable equilibria for organic reactions were investigated in a natural low-temperature serpentinizing continental system. Serpentinization is a water-rock reaction which generates hyperalkaline, reducing conditions. Thermodynamic calculations were performed for reactions between dissolved inorganic carbon and hydrogen to produce methane, formate, and acetate. Quantifying conditions that satisfy equilibrium for these reactions allows subsurface conditions to be predicted. These calculations also lead to hypotheses regarding active microbial processes during serpentinization. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2017

Bryophytes form an important component of northern vegetation communities. Mosses efficiently capture aerially deposited nutrients, restricting nutrient availability to the soil. Given that key ecosystem processes of northern ecosystems are nutrient-limited, understanding nutrient cycling of the moss layer is key to understanding ecosystem nutrient and C cycling in these systems. However, the role of the moss layer in regulating ecosystem-scale nutrient and C cycling, while potentially significant, is largely unknown. The aim of this thesis is to investigate the effect of the relative availability of N and P on aspects of bryophyte nutrient uptake, retention and C acquisition. The hypothesis investigated is that the availability of one nutrient will influence the demand for the other and thereby moss nutrient acquisition and retention mechanisms. To test this hypothesis, various aspects of moss nutrient cycling in response to the relative availability of N and P were investigated. As the C cycle is tightly linked to the N and P cycles, the hypothesis extended to include bryophyte C assimilation and decomposition processes of an arctic tundra. Bryophyte nutrient demand was chiefly governed by the tissue N:P ratio. Consequently, nutrient uptake, both from aerially deposited nutrients and through moss-cyanobacteria N2 fixation, and nutrient losses after a simulated rainfall event were mostly in response to the relative availability of N and P rather than the availability of one nutrient alone. This thesis provides novel evidence that ectohydric mosses have the ability to internally translocate nutrients. In conjunction with efficient nutrient capture, this trait makes mosses strong nutrient sinks which are likely to exert considerable control over ecosystem nutrient cycling. The relative availability of N and P played a role in C uptake of mosses. Through the production of recalcitrant litter and their insulating effect on soil microclimate mosses exerted an influence over ecosystem C cycling.

abstract: Black carbon (BC) is the product of incomplete combustion of biomass and fossil fuels. It is found ubiquitously in nature and is relevant to studies in atmospheric science, soil science, oceanography, and anthropology. Black carbon is best described using a combustion continuum that sub-classifies BC into slightly charred biomass, char, charcoal and soot. These sub-classifications range in particle size, formation temperature, and relative reactivity. Interest in BC has increased because of its role in the long-term storage of organic matter and the biogeochemistry of urban areas. The global BC budget is unbalanced. Production of BC greatly outweighs decomposition of BC. This suggests that there are unknown or underestimated BC removal processes, and it is likely that some of these processes are occurring in soils. However, little is known about BC reactivity in soil and especially in desert soil. This work focuses on soot BC, which is formed at higher temperatures and has a lower relative reactivity than other forms of BC. Here, I assess the contribution of soot BC to central AZ soils and use the isotopic composition of soot BC to identify sources of soot BC. Soot BC is a significant (31%) fraction of the soil organic matter in central AZ and this work suggests that desert and urban soils may be a storage reservoir for soot BC. I further identify previously unknown removal processes of soot BC found naturally in soil and demonstrate that soil soot BC undergoes abiotic (photo-oxidation) and biotic reactions. Not only is soot BC degraded by these processes, but its chemical composition is altered, suggesting that soot BC contains some chemical moieties that are more reactive than others. Because soot BC demonstrates both refractory and reactive character, it is likely that the structure of soot BC; therefore, its interactions in the environment are complex and it is not simply a recalcitrant material. / Dissertation/Thesis / Ph.D. Chemistry 2013