abstract: Lipids perform functions essential to life and have a variety of structures that are influenced by the organisms and environments that produced them. Lipids tend to resist degradation after cell death, leading to their widespread use as biomarkers in geobiology, though their interpretation is often tricky. Many lipid structures are shared among organisms and function in many geochemical conditions and extremes. I argue it is useful to interpret lipid distributions as a balance of functional necessity and energy cost. This work utilizes a quantitative thermodynamic framework for interpreting energetically driven adaptation in lipids. Yellowstone National Park is a prime location to study biological adaptations to a wide range of temperatures and geochemical conditions. Lipids were extracted and quantified from thermophilic microbial communities sampled along the temperature (29-91°C) and chemical gradients of four alkaline Yellowstone hot springs. I observed that decreased alkyl chain carbon content, increased degree of unsaturation, and a shift from ether to ester linkage caused a downstream increase in the average oxidation state of carbon (ZC) I hypothesized these adaptations were selected because they represent cost-effective solutions to providing thermostable membranes. This hypothesis was explored by assessing the relative energetic favorability of autotrophic reactions to form alkyl chains from known concentrations of dissolved inorganic species at elevated temperatures. I found that the oxidation-reduction potential (Eh) predicted to favor formation of sample-representative alkyl chains had a strong positive correlation with Eh calculated from hot spring water chemistry (R2 = 0.72 for the O2/H2O redox couple). A separate thermodynamic analysis of bacteriohopanepolyol lipids found that predicted equilibrium abundances of observed polar headgroup distributions were also highly correlated with Eh of the surrounding water (R2= 0.84). These results represent the first quantitative thermodynamic assessment of microbial lipid adaptation in natural systems and suggest that observed lipid distributions represent energetically cost-effective assemblages along temperature and chemical gradients. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2018

This project focused on Cu-Ni-PGE mineralization and petrogenesis of mafic-ultramafic intrusions in the western Quetico and Wabigoon Subprovinces of the Superior Province. Two intrusions were singled out for detailed study: the Legris Lake Complex, part of circular series of mafic-ultramafic complexes, which includes the Lac des Iles Complex, located in the Wabigoon Subprovince, and the Samuels Lake Intrusion, part of the Quetico Intrusions, located in the Quetico Subprovince. Legris Lake complex. The Legris Lake Complex is a northeast-trending 7.3 by 3.5 kilometre mafic-ultramafic intrusive complex. It is part of a circular series of mafic-ultramafic complexes, the most notable of which is the Lac des Iles Complex, which is host to Canada's only palladium mine. The Legris Lake Complex consists of mostly gabbroic rocks, but also contains lithologies ranging from anorthosite to wehrlite, and, variety of igneous breccias. The gabbroic rocks vary from melanogabbro to porphyritic leucogabbro. Medium grained, massive, biotite-rich leucogabbro is the predominant exposed variety and probably caps the complex. Samuels Lake intrusion. The Samuels Lake intrusion, ca 2688 +6/-5 Ma, located in the centre of the Quetico Subprovince possesses a northeast-southwest elliptical form (500 m by 250 m) and displays rough concentric zoning with a wehrlite core grading into clinopyroxenite border zone, which has been intruded by later homblendite. Olivine-rich rocks commonly contain blebs of pyrrhotite + chalcopyrite + pentlandite with anomalous PGE values, ranging from 50 to 300 ppb, whereas the clinopyroxenite border zone contains disseminated to blebby PGE-rich Cu-sulphide mineralization. (Abstract shortened by UMI.)

Water level changes due to the decommissioning of hydro-electric dams can result in sediment exposure to air. Oxidation of sediments can decrease the pH as a result of iron sulfides changing into iron oxides. The present study was designed to simulate drying and wetting cycles of shallow lake sediments from two lakes (Stump and Black Donald Lakes in Ontario), in order to assess the mineralogical changes of Fe-rich minerals. Our results indicate that the total reactive iron fraction of the sediment increased after the wetting and drying cycles. This increase was caused by the weathering of pyrite and Fe-silicates and their subsequent transformation into more Fe-reactive mineral species. The pH of the surface sediments also decreased following the addition of simulated rainwater and the oxidation of iron sulfides in the sediments. This preliminary study shows that the decommissioning of hydro-electric dams will have an effect on the biogeochemical cycles of iron and sulfur.

Large accumulations of bacteriogenic iron oxides (BIOS) form near Fe(II)-rich groundwater springs in a freshwater wetland located at Chalk River, Ontario, Canada, covering an area of approximately 12 000 m2. BIOS are efficient sorbent and may potentially serve as an in situ bioremediation method to sequester contaminants, such as heavy metals (e.g. Sr2+ and potentially radioisotopes, 9OSr 2+, 129I- and 14C), present in the groundwater. This study focused on the aqueous geochemistry of the wetland, as well as, the solid phase biogeochemistry of BIOS sediments. The mineralogy of BIOS was mainly composed of poorly ordered 2-line ferrihydrite, with minor amounts of lepidocrocite. Goethite was also detected in sediment samples collected during the warmer seasons at two of the sites. Crystallinity of the reactive solid phase Fe in BIOS increased downstream (approx. 10m) from groundwater discharge areas, whereas, Fe(III) became less bioavailable. Analyses of surface water sampling revealed that dissolved Fe(II) and dissolved inorganic carbon (DIC) were significantly correlated (r s =0.83). These two parameters are thought to be involved in a complex biogeochemical cycling in BIOS-rich environments. Both, dissolved Fe(II) and DIC are consumed by chemosynthesis used by iron-oxidizing bacteria during the formation of BIOS or produced during the microbial reduction dissolution of Fe(III)-oxides coupled with the oxidation of organic matter. These results provided valuable information concerning the long term redox stability of BIOS in the natural environment.

The aim of this dissertation, based on three papers, is to utilize novel analytical techniques to examine the potential of non-traditional geochemical proxies, such as calcium and boron isotopes, to address questions related to earth system science. The first paper presents analytical protocols for high-precision calcium isotope measurements using thermal (TIMS) and plasma ionization mass spectrometry (MC-ICP-MS). These are applied to determine calcium isotope abundances of the Late Mesozoic belemnites that, in turn, are used to reconstruct the isotope composition of paleo-seawater and the evolution of the oceanic calcium cycle. The second paper discusses in details the history of the oceanic calcium isotope budget during the Phanerozoic (last ∼500 Ma), which is based on the analysis of calcium isotope compositions of several hundred marine skeletal carbonates, mostly brachiopods, measured by the TIMS technique. The observed experimental record is simulated using a numerical model of coupled calcium/carbon/magnesium global cycles and the results are discussed in the context of changing fluxes of major cations to the oceans. The third paper aims to utilize boron isotopes to constrain temporal changes in pH of the Jurassic surface oceans, with the ultimate goal to evaluate the effect of seawater pH on the oxygen isotope (delta18O) composition of coeval belemnites, hence on the delta18O-based paleo-temperature estimates. Overall, the results of this thesis demonstrate the usefulness and limitations of calcium and boron isotope proxies for studies concerning the evolution of earth system, specifically oceans and the atmosphere, over geological time scales.

Microbial mats are synergistic microbial consortia through which major elements, including sulfur, are cycled due to microbial and geological processes. Depth profiles of pH, O2, sulfide, exopolymeric substances (EPS), and the rate of sulfate reduction were determined in a Microcoleus -dominated marine microbial mat at the Great Sippewissett salt marsh, Massachusetts. In addition, measurements in spirochete enrichments and Spirochaetae litoralis cultures showed sulfide consumption during which polysulfides, thiosulfate, and presumably sulfate formed. These data suggest that spirochetes can play a role in the cycling of sulfur in these mats. The obligate to facultative anaerobic spirochetes consume sulfide to remove oxygen. Furthermore, spirochetes may enhance preservation of microbial mats within the rock record by degrading EPS and producing low molecular weight organic compounds (LMWOC). Both sulfide oxidation (i.e. oxygen removal) and EPS degradation (i.e. production of LMW organic compounds) stimulate the activity of sulfate-reducing bacteria (SRB), which are responsible for the precipitation of calcium carbonate in most lithifying mats.

Acid mine drainage (AMD) is an acidic, iron-rich leachate that causes the dissolution of metals. It constitutes a worldwide problem of environmental contamination detrimental to aquatic life and water quality. AMD, however, is naturally attenuated at Davis Mine in Rowe, Massachusetts. We hypothesize that sulfate-reducing bacteria (SRB) are attenuating AMD. To elucidate the mechanisms by which SRB attenuate AMD, three research projects were conducted using a suite of molecular and geochemical techniques. First we established biological influence on the attenuation of AMD by comparing the microbial community and geochemical trends of microcosms of two contrasting areas within the site: AMD attenuating (AZ) and AMD generating (GZ) zones. The differences in geochemical trends between these zones were related to differences in microbial community membership. SRB were only detected in microcosms of the AZ, while iron oxidizers were only detected in the GZ. This study indicates that biological activity contributes to the attenuation of AMD and that SRB may have a role. To further describe the role of SRB, we determined the rates of sulfate reduction, the abundance, and membership of SRB in the second project. The sulfate reduction rate was weakly correlated with the abundance of SRB. This indicates that the SRB population may be utilizing another electron acceptor. One such electron acceptor would be iron, which was investigated in the third project. When SRB are inhibited, neither accumulation of reduced iron nor the formation of reduced iron sulfide precipitates occurred. Higher concentration of sulfide produced an increase in reduced iron and pH. Therefore, iron reduction mediated by reaction with biogenic sulfide contributes to the attenuation of AMD. This is the first report of the biological enhancement of iron reduction by acidotolerant SRB. The interdisciplinary research described in this dissertation provides evidence that SRB attenuate AMD through sulfate and iron reduction and a greater understanding of SRB in acidic environments. It also demonstrates how the biogeochemical cycling of sulfur is coupled to the iron cycle. Overall, the ubiquity and metabolic versatility of SRB offers boundless potential and exciting opportunities of study in the fields of bioremediation, geomicrobiology, and microbial ecology.

The reduction of Fe(III) is one of the most significant reactions that takes place as anaerobic conditions develop in soils and sediments. The mechanisms by which Fe(III) is reduced in sediment and by pure cultures was examined in the research. Other than by direct contact between Fe(III) reducing microorganisms and Fe(III) oxide minerals, there are two ways Fe(III) oxide can be reduced. Fe(III) oxide reduction can occur without contact via electron shuttling by an environmental or microbially produced molecule or by chelation of Fe(III) by an environmental or microbially produced molecule. Both the environment and cultures were examined for these phenomena. Humics and humic analogs were found to serve as electron shuttles between Fe(III) oxides and Fe(III) reducing microorganisms in aquifer sediments while, other compounds found to serve as electron shuttles in culture did not function as electron shuttles in soils and sediments. Environments where humus materials are capable of serving as electron shuttles were located. Environments also existed where there were appreciable amounts of soluble Fe(III), indicating that chelators are present in these environments. The Fe(III) reducing microorganism Geobacter metallireducens was found to reduce Fe(III) oxides only via direct contact. The method used previously to assay for reduction of Fe(III) minerals without contact, dialysis tubing, was shown to be invalid. Another method was developed, by which Fe(III) oxides were entrapped in alginate beads. This method together with, cell suspensions, thin layer chromatography and soft agar plates were used to assay for the electron shuttling capacity. Both Geothrix ferrnentans and Shewanella alga strain BrY where found to produce both electron shuttles and Fe(III) chelators, thus eliminating the need for contact between Fe(III) mineral and these Fe(III) reducing microorganisms thus exhibiting methods of Fe(III) reduction different from Geobacter metallireducens.

Sustainability is one of the biggest goals of humankind in the new millennium. An increasing global demand on agricultural products stimulates agricultural expansion in Brazil, especially in the Southwestern Amazon, namely in the Cerrado and Amazon biomes. A better understanding of biogeochemical cycles and their influence on natural and agricultural systems is key to achieve environmental sustainability and improve agricultural efficiency. These biogeochemical cycles are driven by microbes, and the aim of this thesis was to correlate microbial functional group abundances with differences in carbon, nitrogen, and greenhouse gas cycles in response to land use changes in Southwestern Amazon soils. This work was performed at the University of São Paulo, Brazil, and at the University of Massachusetts Amherst, USA, while the candidate was enrolled in Ph.D. programs at both universities. The thesis is composed of five studies. The first study shows that land use change from Cerrado and forest to agriculture (soybean, Glycine max (L. Merrill), in succession with other crops) or pasture (Brachiaria brizantha (Hochst. ex A. Rich.) did not reduce soil microbial diversity but changed microbial structure. The second study, a physico-chemical background for this land use conversion, describes the alteration of C and N stocks, soil chemical parameters, and microbiological parameters such as biomass, biological C stocks, and changes in the abundance of prokaryotes and fungi. In the third and fourth studies microcosm experiments depict how the agricultural change to soybean and Brachiaria alter the original microbial structure found in forest or cerrado. These studies focused on abundances of key biogeochemical genes (amoA, nirK, nirS, norB, nosZ, mcrA, and pmoA) and correlated gene copy abundances with C, N, and GHG measurements. In the fifth study, in situ soil surveys and GHG samplings were used to characterize the changes from forest to pasture (B. brizantha , 25 years) or soybean crop system (for 2 years or 25 years in succession). We found correlations between genes and processes, indicating that gene abundances provide important microbial information for the understanding of the targeted biogeochemical cycles. Land use, rather than plant species, promotes alterations in microbial gene abundances and processes. During the survey period, forest exhibited higher microbial activity, resulting in higher nitrate availability and N2O emissions. These processes were correlated with higher abundances of process related genes. Nitrate and N2O emissions were lower in agricultural and pasture soils. CO2 emission was higher in the two-year-old soybean plot. The forest and two-year-old soybean plots acted as a sink for CH4, while the pasture plots represented a source of it. The results validated the use of gene abundance determination as a valuable tool to better understand C, N, and GHG processes. The genes nirK, nosZ, and 16S rRNA presented the best correlations with the processes. A larger temporal and spatial analysis is needed to infer statements on the processes' dynamics due to land use change. For the first time gene abundance measurements were used to integrate the C, N and GHG cycles, giving insights into land use changes in Southwestern Amazon.

Ocean environments are being impacted by climate warming, elevated carbon dioxide (CO2) levels, and shifting nutrient sources and sinks. It is essential to quantify the sensitivity of microorganisms to these effects of global change because they form the base of the marine food web and are an integral component of nutrient cycling on the planet. their role in photosynthesis, nutrient uptake, and transfer of organic matter into higher trophic levels or to the deep ocean via the biological pump render microorganisms key in ecosystem structure and function and in regulating the global climate. The goal of this dissertation research was to determine how changing environmental conditions impact microbial communities and the rates at which they take up nutrients. Research for this dissertation took place in the Southern California Bight and in the Ross Sea, Antarctica, where fully factorial designs were used to investigate the response of microorganisms to multiple global change parameters. Nutrient uptake rates were measured using 13C and 15N stable isotopes for carbon and nitrogen substrates and 33P radioisotopes for phosphorus substrates. In the Southern California Bight, a microbial assemblage was collected and incubated in an ‘ecostat’ continuous culture system, where elevated temperature, CO2, and the dominant nitrogen substrate (nitrate or urea) in the diluent were manipulated. During this experiment uptake rates of dissolved inorganic carbon (DIC), nitrate (NO3-), and urea were determined for two microbial size classes (0.7-5.0 μm and >5.0 μm). Urea uptake rates were greater than NO3-, and uptake rates of urea and DIC for both size fractions increased at elevated temperature, while uptake rates of NO3- by smaller microorganisms increased when CO2 levels were high. In the Ross Sea, the impact of elevated temperature, CO2, and iron addition on DIC and NO3- uptake rates by two size classes (0.7-5.0 μm and >5.0 μm) of a late-season microbial community were investigated using a semi-continuous and continuous ‘ecostat’ culturing approach. Temperature impacted the microbial community the most, significantly increasing NO3- and DIC uptake rates by larger microorganisms. The effects of iron addition were more apparent when temperature was also elevated, and CO2 did not impact rates. Bioassay experiments were also conducted in the Ross Sea to determine how increasing and decreasing the N:P supply ratio in combination with other parameters (temperature and iron) impact uptake rates of DIC, NO3-, and amino acids. Results from these experiments show that changes to the dissolved N:P supply ratio have the potential to alter nutrient uptake rates over short time scales, but that temperature elevation and iron addition have a larger impact. Additional experiments were completed on diatoms (Fragilariopsis cylindrus and Pseudo-nitzschia subcurvata) and Phaeocystis antarctica, three important phytoplankton species collected from the Ross Sea, to assess how temperature elevation and iron addition impact uptake rates of a number of inorganic and organic carbon, nitrogen, and phosphorus substrates. These culture studies generally show that when temperature is increased, diatoms are able to take up nutrients more rapidly than Phaeocystis antarctica. Results from this dissertation show that nutrient cycles and phytoplankton communities in the Southern California Bight and the Ross Sea, Antarctica will likely be different in the future. Although all variables tested were found to exert some influence on microbial nutrient cycling, temperature elevation generally had the largest effect, increasing biomass and uptake rates, structuring the composition of the microbial community, and altering stoichiometry. This research did not include top down effects and it is limited spatially and temporally, however, it demonstrates the importance of studying different nutrient substrates and looking at multiple interactive stressors to gain a more comprehensive view of potential change.