<p> <i>Polylepis</i> forests are a unique high-elevation forests dominated by trees of the <i>Polylepis</i> (Rosaceae) genus found only in South America. These forests are distinctive not only for growing at some of the highest elevations in the world, but because they are distributed as isolated forest islands inside a landscape otherwise dominated by grasses. This distribution is due in part to human disturbance on the landscape and there is interest in restoring cover of <i>Polylepis</i>. Understanding of regeneration dynamics and seedling ecology of <i>Polylepis</i> can help in the management of forests and the restoration of this forest cover, but there are important gaps in knowledge regarding theses aspects in most species. For the expansion of forest cover into current grassland areas, it is important to understand the ability of seedlings to colonize, survive and grow in these areas and identify important biotic and abiotic barriers to this. In this dissertation, I contribute to our understanding of these ecological aspects for two species of <i>Polylepis</i> (<i>P. sericea </i> and <i>P. weberbaueri</i>) using a series observational studies and manipulative experiments in forests found between 4000&ndash;4500 masl in Huascaran National Park (Ancash, Peru). </p><p> In Chapter 1, I surveyed patterns of seedling dispersion across forest-grassland boundaries along the elevational gradient and identified significant associations of seedling densities to environmental covariates at local and landscape scales. I found that seedling densities of both species decrease drastically at the edge of the forest canopy, and few seedlings are found in the grassland even within meters of the forest, suggesting significant barriers to seedling establishment in the grassland. Additionally, seedling densities of each species showed patterns with elevation and solar irradiation that mirrored those of adult distributions on the landscape and were different from each other, suggesting that each species has unique environmental tolerances that manifest in the seedling stage and are important to consider in their management and restoration. </p><p> In Chapter 2, I used a series of livestock exclusion experiments to examine the influence of domestic livestock on natural regeneration inside and outside the forest and test the hypothesis that livestock are a significant barrier to seedling establishment at forest-grassland edges. After one year of livestock exclusion, I found only partial support for this hypothesis. In <i>P. sericea</i> forest stands, seedling densities increased, and recruitment and seedling growth was higher in fenced grassland areas. However, in <i> P. weberbaueri</i> stands there was little change in juvenile densities and no differences in seedling performance, except that recruitment was lower in fenced forests areas compared to unfenced forest. This showed that the influences of livestock on <i>Polylepis</i> seedling may be different depending on the habitat and species of <i>Polylepis</i>. Additionally, we found that seedling survival was surprisingly high, and similar between forest and grassland habitat. </p><p> In Chapter 3, I used sowing and &ldquo;wildling&rdquo; transplant experiments within the previous exclosure experiments to tease apart early ontogenetic filters to seedling establishment in the grassland compared to the forest. I found that the seedling emergence stage is a strong bottleneck for seedling establishment in the grassland. Furthermore, I found that <i>P. weberbueri </i> seedling density inside the forest appears to be seed limited, and can be increased by sowing. Transplanted seedlings survival was lower than found previously for natural seedlings, but was also similar between both habitats. However, it appears that livestock depresses <i>P. sericea </i> transplant survival inside the forest. Only <i>P. weberbueri </i> seedlings showed differences in growth between habitats, declining in height in the grassland, but there was only evidence that livestock suppressed growth. I concluded that seedling transplant will be the most efficient way to increase seedlings in the grassland for restoration. </p><p> Together, the results of this dissertation suggest that both unassisted and assisted expansion of natural <i>Polylepis</i> forests faces significant barriers, in particular low seedling emergence in grassland is a strong bottleneck to establishment in this habitat. It remains unclear whether livestock are generally a barrier to forest expansion, as their effects appear to be specific to each species of <i>Polylepis</i>. Here, <i> P. sericea</i> appears to be more sensitive in both forest and grassland to livestock activity than <i>P. weberbaueri</i>, but future work should address longer-term effects of livestock exclusion to confirm the population trajectories observed after one year. Finally, wilding transplants of these species can be used in restoration to overcome the barrier emergence poses to <i>Polylepis</i> establishment in grassland, although with further research, seeding schemes may prove a viable strategy</p><p>

<p> Biochar was produced from the fast pyrolysis of Douglas fir (DBC). Magnetic biochar (MDBC) was synthesized by mixing aqueous biochar suspensions with an aqueous Fe³⁺/Fe²⁺ solution, followed by NaOH treatment, which causes precipitation of magnetite, Fe3O4 onto DBC. The DBC and the resulting MDBC were investigated as potential green adsorbents for lead remediation from the water. The surface chemistry of both chars was examined by SEM, SEM-EDX, TEM, PZC, and surface area measurements. Batch sorption studies were carried out at 25 &deg;C, from pH 2-7 and with adsorbate concentration range of 50-200 mg/L. Maximum lead removal due to adsorption occurred at pH 5 for both DBC and MDBC. DBC was removed using filtration, whereas MDBC was removed magnetically. Remediated solutions were analyzed using atomic adsorption spectroscopy (AAS). Lead batch sorption studies were also conducted to study the effect of water hardness on rate and equilibrium data at different adsorbate concentrations to construct equilibrium isotherms. Three levels of water hardness were employed; low (30 mg/L), medium (90 mg/L) and high (150 mg/L). Sorption performances at 25 &deg;C were evaluated using Langmuir and Freundlich adsorption isotherm models. The maximum Langmuir adsorption capacity at pH 5 and 25 &deg;C for low, medium and high hard water were 106.54, 85.65 and 76.70 mg/g for DBC and 69.93 mg/g, 64.88 mg/g and 63.03 mg/g for MDBC. DBC and MDBC were also successfully applied for lead removal from natural water samples. Both chars can be used as potential low-cost green adsorbents for lead remediation.</p><p>

<p> Climate change is arguably the biggest challenge facing humanity. Successful mitigation and adaption planning vitally requires more science in regard to its impacts on ecological systems. To address knowledge gaps regarding climate change impacts within the regional level, I performed a series of analyses on an "early responder" species in the Greater Yellowstone Ecosystem and examine how its distribution may be impacted by biotic and abiotic factors. My research aids in decision making processes for regional land managers that must address climate change in their policy decisions and increases ecological understanding at a landscape level. </p><p> This manuscript includes a detailed analysis of past, present, and projected climate in the Greater Yellowstone Ecosystem. I addressed the expected impacts of present and future climate shifts on the distribution of the sub-alpine tree species, whitebark pine (<i>Pinus albicaulis</i>) and its main disturbance agent, mountain pine beetle (<i>Dendroctonus ponderosae</i>). This research found a major reduction of suitable climate habitat for <i> P.albicaulis</i> within the Greater Yellowstone Ecosystem under multiple Global Circulation Models and Representative Concentration Pathway futures. Finally, this research determined that the recent <i>D.ponderosae</i> outbreak driven by climate effects in 2000&ndash;2010, that resulted in an unprecedented mortality event on <i>P.albicaulis</i> was more than double the risk area size of any previous outbreak since 1951. Although more studies are necessary to reduce uncertainty and make assertive recommendations for management actions, this research suggests that future sub-alpine stand structure and composition may be radically different than anything in recent history due to range shifts of suitable climate habitat and disturbance agents, and advocates for land managers to apply a multifaceted approach of competitor thinning and controlled burning to ensure the resilience and persistence of <i> P.albicaulis</i>.</p><p>

<p> High elevation, mountainous regions have a high concentration of mining activities and resulting acid mine drainage (AMD) that is typically acidic and often contains elevated concentrations of metals. The impacts of AMD on denitrifying microbial communities is not well understood, despite these organisms&rsquo; central role in the nitrogen cycle, contribution to greenhouse gas production, and potential to provide ecosystem services through the mitigation of nitrogen pollution. This study examined denitrifying microbes across four regions within the Iron Springs Mining District (13 sites over four time-points) located in Southwest Colorado at high elevation that receive AMD or naturally-occurring acid rock drainage (ARD). Denitrification functional gene sequences (<i> nirS</i> and <i>nirK</i> coding for nitrite reductase) had a high number of observed OTUs (260 for <i>nirS</i> and 253 for <i> nirK</i>) and were observed at sites with pH as low as 3.2, dissolved oxygen as low as 1.0 mg/L, and metals >10 mg/L (including aluminum, iron, manganese, and zinc). A majority of the <i>nirK</i> and <i> nirS</i> OTUs (> 60%) were present in only one sampling region. Approximately 8% of the <i>nirK</i> and <i>nirS</i> OTUs had a more cosmopolitan distribution with presence in three or more regions. Phylogenetically related OTUs were found across sites with very different chemistry. The total <i>nirS</i> community structure was correlated to iron, conductivity, sodium, and calcium, which may suggest that these factors play an important role in shaping the <i>nirS</i> community. Overall, these findings improve upon our understanding of the potential for denitrification within an ecosystem impacted by AMD and provide a foundation for future research to understand the rates and physiology of these denitrifying organisms.</p><p>

<p> Concerns over delayed soil warming and drying have hindered adoption of conservation tillage practices in frigid environments. Our objectives were to evaluate the effects of chisel plow (CP), vertical tillage (VT), strip tillage with coulters (STC), and strip tillage with shanks (STS) on soil warming and drying and their potential consequences to crop yields. A two-year study was conduct at three full-scale, producer-managed, corn-soybean fields in the Red River Valley of eastern North Dakota and western Minnesota. Tillage treatments were assessed to measure crop residue cover, soil temperatures, soil volumetric water contents, crop yields, and other metrics. Our study indicated significant differences for many soil physical and chemical parameters, but little to none for soil warming and crop yields. Yield differences were attributed to varying fertilizer management practices, timing, and application method. These findings emphasize the importance of field management practices that compliment conservation tillage for obtaining competitive crop yields. </p><p>

<p> Rhizobia are soil bacteria that can associate with some legumes and participate in symbiotic nitrogen fixation. Bacterial CspA family members are small, single stranded nucleic acid binding proteins conserved throughout all domains of life. Here, the role of CspA family proteins in the symbiotic development of <i>Sinorhizobium meliloti</i> with <i>Medicago sativa</i> (alfalfa) is investigated. Expression and genetic deletion strain analysis revealed that CspA family proteins are differentially expressed in symbiosis and contribute to symbiotic effectiveness. RNAseq analysis of native co-immunoprecipitated RNAs identified a novel interaction between several CspA family proteins and the &alpha;R14 family of small non-coding RNA (sRNAs). Whole transcriptome analysis defined transcriptional defects associated with loss of CspA function. The development of a new <i>in vitro</i> RNA binding assay using broccoli, a Green Fluorescent Protein (GFP) RNA mimic, is described as well as its use in defining binding specificity of CspA family proteins with synthetic and native ?R14 family sRNA structures. This work concludes that CspA family proteins interact with and influence the stability of specific RNA structures and these interactions control RNA regulated processes important for symbiotic development.</p><p>

<p> Man-made pollution is hazardous to both the environment and human health. This study attempts to develop a low-cost, biobased adsorbent for CO₂ capture and heavy metal removal. The adsorption behavior of CO₂ from air and Pb (II) from aqueous systems onto polyethylenimine (PEI) modified biochar was studied. Chemical and physical pretreatments were performed in an attempt to enhance the adsorption kinetics of biochar. FT-IR and Elemental Analysis were performed to confirm the loading of PEI onto the surface of biochar was achieved. The efficiency of the PEI modified biochar on the removal of Pb (II) from aqueous solutions was determined by Atomic Absorption Spectrometer (AAS). Alkali pretreatment of PEI modified biochar increased CO₂ capture and removal of Pb(II). This experiment introduces a new approach to air and water purification by using the combination of an amine with biochar.</p><p>

<p> The expression &ldquo;no man is an island&rdquo; is intended to represent human isolation in its most extreme form depicting man as an isolated body of land. Contrary to the statement, an element unnoticed within this expression frequently is the existence of that Island. The expression is intended as an example of articulating absolute isolation of the human in existence. However, the idea of the human being a location being the island is still declared. As humans who inhabit this earth, we cannot exist without space. There is an undeniable link between the spaces and the inhabitants within them. As a result of Modernity, the majority of the human inhabitants of the world exist throughout their entire lives within the Built Environment. The Built Environment holds an assortment of spaces that have been composed in order to accommodate our existence. A practice of engaging the composition of these spaces for human inhabitance is commonly what is known as Architectural Design. Spaces will continue to exist and Architecture is a mean of addressing the design of them. Understanding these spaces through their Concepts, Conditions, and Components allows for a classification of common spaces that exist within the Built Environment. The classification of these spaces within the Built Environment arrives at the mutual dialogue of the Built Environment Spatial Layers. The ever-demanding human population that is growing exponentially cause many ecological, economical, and social dilemmas through our modern interpretations of spaces composed within the Built Environment. Understanding the Built Environment through the Built Environment Spatial Layers allows for the acknowledged design surrounding these spaces that yield the greatest sustainability through energy efficiency and minimizing environmental impacts without denying the humanity of that concept.</p>

Two strains of Clostridium hungatei sp. nov., a cellulolytic, N$\sb2$-fixing bacterium were isolated from samples of soil rich in decaying plant material. On the basis of comparisons of their morphological, physiological and phylogenetic characteristics, and of their G + C mol % content, with those of other Clostridium species, it was concluded that the two strains (designated strain AD and strain B3B) were representatives of a novel species of Clostridium. C. hungatei produces an extracellular cellulase complex which exhibits cellulase (i.e., Avicelase, carboxymethylcellulase) and xylanase activities. The cellulase-xylanase complex biosynthesis, in C. hungatei, was induced when cells of strain AD were grown with soluble products of cellulose hydrolysis (e.g., cellobiose) as the carbon and energy source. Induction of cellulase-xylanase complex, above a low constitutive level, occurred when the cellobiose concentration was 0.1% (wt/vol) or lower, but not at higher concentrations. Induction above the constitutive level was not observed when other soluble sugars (e.g., D-mannose) served as carbon and energy source. Cellulase activity of the cellulase-xylanase complex produced by C. hungatei is inhibited by cellobiose (at concentrations as low as 0.02%, wt/vol). Growth kinetics, cellulose degradation studies and enzyme assays revealed that supernatant fluid samples of C. hungatei cultures growing under N$\sb2$-fixing conditions, or at low dilution rates (in a chemostat limited by carbon and energy source) in the presence of NH$\sb4$Cl showed higher cellulase activity per cell mass produced as compared to cultures growing in the presence of combined nitrogen or at higher dilution rates. In nature, the ability to regulate the cellulase-xylanase complex synthesis, and the ability to enhance cellulase activity per cell mass produced under conditions of higher energy demand (e.g., N$\sb2$ fixation) may give C. hungatei an advantage over other bacteria living in the same environment. A N$\sb2$-fixing stable coculture, consisting of C. hungatei strain AD and a facultatively anaerobic, non-cellulolytic bacterium (strain CU-1), was used as a model to determine whether extracellular cellulases produced by cellulolytic bacteria may serve as nitrogen sources for non-N$\sb2$-fixing bacteria growing in heterogeneous microbial communities. Inasmuch as supernatant fluids of cocultures showed lower cellulase and xylanase activities as compared to clostridial monoculture supernatants, and supernatant fluids of strain CU-1 showed proteolytic activity when grown in the presence of sources of amino acids (e.g., C. hungatei's cellulase system), and of the basis of other evidence it was concluded that, in anaerobic environments deficient in combined nitrogen, extracellular cellulases may serve as nitrogen sources for non-N$\sb2$-fixing bacteria. In addition, strain CU-1 grew in monoculture in a chemically-defined cellobiose-containing medium to which a gel-filtration purified strain AD cellulase preparation was added as the only nitrogen source. Using a cellulolytic methanogenic coculture, composed of C. hungatei strain AD, and a strain of H$\sb2$-consuming methanogen (e.g., Methanobacterium formicicum strain WH), the effects of interspecies H$\sb2$ transfer on growth, cellulose degradation and product formation were studied. The results indicated that interspecies H$\sb2$ transfer enhances growth rate and affects product formation by the cellulolytic clostridium, and indirectly stimulates cellulose degradation.

The purpose of this study is to describe the impact of mine effluent on its environment, and to determine the processes, which influence the geochemistry of the spoil and of surface and groundwater in the Davis Mine Valley. The Davis Pyrite Mine is one of the small abandoned mines in the Berkshire Mts., in Massachusetts. Since the collapse of the mine, in 1911, forest has reclaimed its surroundings, yet the acid mine effluent still affects nearby streams. The spoil and the Davis Mine Creek watershed is a small area enclosed by rocks having minimal carbonate content. It has been untouched by humans for 80 years so the place is ideal for the study of the natural geochemical processes that control such environments. The surface and shallow ground-water in the Davis Mine Valley have low pH (3.28) and high total dissolved solid content. The upper 30–35 cm of the spoil pile is depleted in sulfide and silicate minerals, while it is enriched in iron-oxyhydroxide minerals. The amount of silicate minerals increases with depth. Three main processes determine the mineralogy, geochemistry, and hydrochemistry of the spoil in such a low buffer-capacity environment: (1) The bacterially catalyzed oxidation of pyrite is continuous, so it constantly produces low-pH water and high iron content. The acid water further dissolves minerals hence elevating metal-ion concentrations. (2) The water inflow with a relatively higher pH (rain, snowmelt, unaffected surface and subsurface water) flushes the freshly precipitated soluble constituents, and it dilute the element concentrations in the mixed water meanwhile increasing its pH. This process then enhances adsorption and precipitation. (3) The dynamic dissolution and precipitation of various iron-oxyhydroxides control the iron content of water and buffer the pH between 2.5 and 3.5. This low pH inhibits metal ion adsorption on mineral surfaces. Local formation of a surface hardpan layer modified chemical processes in the groundwater. This layer is built up from a crust of goethite and jarosite with low permeability that inhibits O2 diffusion and surface water infiltration.