<p>Investigating the presence of microbial communities in the Earth's deep terrestrial subsurface and the metabolic processes taking place in these environments provides insight into the some of the ultimate limits for life on Earth, as well as the potential for microbial life to exist within the subsurface of other planetary bodies. This Master's thesis project utilized phospholipid fatty acid (PLFA) analysis, in combination with carbon isotope analyses (δ¹³C and Δ¹⁴C), to explore the presence and activity of microbial communities living within deep terrestrial subsurface fracture water systems and low permeability, deep sedimentary rocks. Deep fracture water systems, ranging from 0.9 to 3.2 km below land surface, were sampled for microbial communities via deep mine boreholes in the Witwatersrand Basin of South Africa. PLFA concentrations revealed low biomass microbial communities, ranging from 2x10¹ to 5x10⁴ cells per mL and the PLFA profiles contained indicators for environmental stressors, including high temperatures and nutrient deprivation. δ¹³C and Δ¹⁴C analyses of PLFAs and potential carbon sources (dissolved inorganic carbon (DIC), dissolved organic carbon (DOC) and methane) identified microbial utilization of methane in some systems and utilization of DIC in others. Evidence for microbial oxidation of methane and chemoautotrophy in these systems is consistent with a self-sustaining deep terrestrial subsurface biosphere that is capable of surviving independent of the photosphere. Viable microbial communities were also identified within deep (334 to 694 m depth) sedimentary rock cores sampled from the Michigan Basin, Canada. PLFA analyses revealed microbial cell densities ranging from 1-3 x 10⁵ cells/mL and identified PLFA indicators for environmental stressors. These results demonstrate the ubiquity of microbial life in the deep terrestrial subsurface and provide insight into microbial carbon sources and cycling in deep microbial systems which may persist in isolation over geologic timescales.</p> / Master of Science (MSc)

The isotopic composition of the organic components of an animal's body, with respect to carbon and nitrogen, reflect the weighted average of the isotopic compositions of the animal's food sources, with a certain degree of enrichment in the heavier isotopes. Thus, by comparing the isotopic compositions of the animal and all the potential food sources, it is possible to ascertain the relative proportions of each availible food source in its diet, if the various food sources are sufficiently isotopically distinct. This approach is particularly usefull in estuarine communities where food-webs tend to be complex and where there are several sources of primary productivity. In this study it was used on two types of claw in an arctic and a temperate estuarine tidal flat in order to assess the importance of terrestrially fixed organic matter to each community. The results indicated that while marine and terrestrial organics were important food sources in the arctic tidal flat, the clams in the temperate site depended mostly on marine organics. / Thesis / Bachelor of Science (BSc)

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The dwarf wedgemussel (Alasmidonta heterodon) is a federally endangered freshwater mussel that once ranged from New Brunswick to North Carolina, but now only exists in isolated populations throughout its diminished range. Laboratory propagation in conjunction with augmentation or reintroduction is considered a critical component of dwarf wedgemussel restoration. My thesis aimed to I) develop in-vitro propagation techniques including methods to minimize microbial contamination for two Alasmidonta species and II) compile and assess critical fish assemblage information at existing dwarf wedgemussel presence and absence locations to inform future restoration activities. For the first objective (Chapter 2) I assessed three methods of contamination mitigation (media change frequency, concentration of the antifungal Amphotericin B, and method of antifungal replenishment). Across all experiments, higher levels of contamination severity had a negative impact on transformation success. In my experiments, dishes that had media changes every other day (vs. those changed daily and every 3 days) had the highest contamination and the lowest glochidia transformation success. Treatments with the lowest (0 µg/mL) concentration of the antifungal, Amphotericin B, and got a low-dose replenishment of Amphotericin B (vs frequent media changes) had the highest transformation success. The fungus was identified as Candida parapsilosis, a common fungus found in aquatic and human environments; future propagation efforts should use mitigation methods that are specific to the fungal contaminant. In the assessment of host fish near dwarf wedgemussel locations (Chapter 3), two fish repeatedly emerged as indicators of dwarf wedgemussel occurrence and abundance: the tessellated darter (Etheostoma olmstedi) and brown trout (Salmo trutta). Tessellated darter was positively related to dwarf wedgemussel which supports the importance of tessellated darter as a host fish in the wild. The negative relationship between dwarf wedgemussel and brown trout may indicate a difference in habitat between the species or brown trout’s predation upon wild hosts. Results from this project will be used in conjunction with habitat and genetic information to inform future restoration plans in the northeast and add to the growing body of literature on in-vitro propagation of freshwater mussels.

The establishment of monoculture plantations of exotic tree species is common practice for supplementing native timber stocks. Such plantations typically provide inferior habitat for wildlife compared to native forest, which may result in a net reduction in biodiversity. However, some studies report that plantations may increase net biodiversity at the landscape scale by introducing novel habitats or supplementing existing natural forests. Using point count surveys, I examined six mature Norway spruce (Picea abies) plantations in western Massachusetts in 2016 and 2017 to evaluate bird use of these habitats relative to native forest stands. Count data were analyzed using N-mixture models to correct for imperfect detection, providing more accurate estimates of true abundance. Our findings showed that overall species richness for spruce plantations was not significantly lower than that of native forest habitats. Red-breasted nuthatch (Sitta canadensis) and golden-crowned kinglet (Regulus satrapa) were most abundant in spruce plantations. Conifer dependent species such as Blackburnian warbler (Setophaga fusca) and brown creeper (Certhia americana), were significantly more abundant in spruce plantations relative to native deciduous, hemlock, and mixed stands. Species that heavily associate with broadleaf habitat were rarely observed in spruce plantations. Species that associate with eastern hemlock habitat, such as Blue-headed vireo (Vireo solitarious) and black-throated green warbler (Setophaga virens) were observed using spruce plantations at similar levels as eastern hemlock stands. These results demonstrate that Norway spruce plantations can provide suitable habitat for native species associated with conifers, which is significant given projected continued decline of eastern hemlock in response to the hemlock wooly adelgid (Adelges tsugae). Although large-scale conversion of native forest to plantations would likely lead to a loss in biodiversity, land managers could be justified in allowing small-scale plantations to persist without suffering negative impacts to native biodiversity.

A commercially available, tripod mounted, ground-based laser scanner was used to assess forest canopies and measure individual tree parameters. The instrument is comparable to scanning airborne light detection and ranging (lidar) technology but gathers data at higher resolution over a more limited scale. The raw data consist of a series of range measurements to visible surfaces taken at known angles relative to the scanner. Data were translated into three dimensional (3D) point clouds with points corresponding to surfaces visible from the scanner vantage point. A 20 m x 40 m permanent plot located in upland deciduous forest at Coweeta, NC was assessed with 41 and 45 scans gathered during periods of leaf-on and leaf-off, respectively. Data management and summary needs were addressed, focusing on the development of registration methods to align point clouds collected from multiple vantage points and minimize the volume of the plot canopy occluded from the scanner's view. Automated algorithms were developed to extract points representing tree bole surfaces, bole centers and ground surfaces. The extracted points served as the control surfaces necessary for registration. Occlusion was minimized by combining aligned point clouds captured from multiple vantage points with 0.1% and 0.34% of the volume scanned being occluded from view under leaf-off and leaf-on conditions, respectively. The point cloud data were summarized to estimate individual tree parameters including diameter at breast height (dbh), upper stem diameters, branch heights and XY positions of trees on the plot. Estimated tree positions were, on average, within 0.4 m of tree positions measured independently on the plot. Canopy height models, digital terrain models and 3D maps of the density of canopy surfaces were created using aligned point cloud data. Finally spatially explicit models of the horizontal and vertical distribution of plant area index (PAI) and leaf area index (LAI) were generated as examples of useful data summaries that cannot be practically collected using existing methods. / Ph. D.

Multiple sections at 13 localities in West Virginia and Virginia, that expose the Early Carboniferous (Late Mississippian) Bluefield, Hinton, and Bluestone Formations, were measured. Geological structures and paleontological occurrences were recorded. In situ rooted plants were compared with transported plant and animal assemblages from fluvially dominated terrestrial beds and interdistributary channel-dominated, bay-fill, marine beds in order to interpret the paleoecology of this subtropical Early Carboniferous coastal landscape. Interdistributary wetlands of the Bluefield, Hinton and Bluestone Formations resemble earlier swamps more than those of the younger Pennsylvanian. In both Hampshire (Late Devonian, Famennian) and Price Formation (Early Carboniferous, Toumaisian) coal swamps, diversity is so low that only one taxon of plant is present: Rhacophyton ceratangium in the Late Devonian and Lepidodendropsis vandergrachtii in the Early Mississippian. The presence of Lepidodendron veltheimii as the apparent sole occupant of these younger Early Carboniferous plant communities makes them most similar to the arborescent lycopod-dominated Price Formation swamps. Although many Pennsylvanian (Late Carboniferous) swamps were also dominated by tree lycopods, including species of Lepidodendron sensu lato, other plants were present as well. Thus, these Late Mississippian communities incorporate some features of both younger and older swamps and can be considered ecologically transitional between them. Swamps have been stressful environments for plant growth for as long as they have existed. This is manifested by their low diversity since the Paleozoic and continues to be true today. / Ph. D.

Stream morphology is an important aspect of many hydrological and ecological applications such as stream restoration design (SRD) and estimating sediment loads for total maximum daily load (TMDL) development. Surveying of stream morphology traditionally involves point measurement tools, such as total stations, or remote sensing technologies, such as aerial laser scanning (ALS), which have limitations in spatial resolution. Terrestrial laser scanning (TLS) can potentially offer improvements over other surveying methods by providing greater resolution and accuracy. The first two objectives were to quantify the measurement and interpolation errors from total station surveying using TLS as a reference dataset for two fluvial applications: 1) measuring streambank retreat (SBR) for sediment load calculations; and 2) measuring topography for habitat complexity quantification. The third objective was to apply knowledge uncertainties and stochastic variability to the application of SRD. A streambank on Stroubles Creek in Blacksburg, VA was surveyed six times over two years to measure SBR. Both total station surveying and erosion pins overestimated total volumetric retreat compared to TLS by 32% and 17%, respectively. The error in SBR using traditional methods would be significant when extrapolating to reach-scale estimates of sediment load. TLS allowed for collecting topographic data over the entire streambank surface and provides small-scale measurements on the spatial variability of SBR. The topography of a reach on the Staunton River in Shenandoah National Park, VA was measured to quantify habitat complexity. Total station surveying underestimated the volume of in-stream rocks by 55% compared to TLS. An algorithm was developed for delineating in-stream rocks from the TLS dataset. Complexity metrics, such as percent in-stream rock cover and cross-sectional heterogeneity, were derived and compared between both methods. TLS quantified habitat complexity in an automated, unbiased manner at a high spatial resolution. Finally, a two-phase uncertainty analysis was performed with Monte Carlo Simulation (MCS) on a two-stage channel SRD for Stroubles Creek. Both knowledge errors (Manning's <i>n</i> and Shield's number) and natural stochasticity (bankfull discharge and grain size) were incorporated into the analysis. The uncertainty design solutions for possible channel dimensions varied over a range of one to four times the magnitude of the deterministic solution. The uncertainty inherent in SRD should be quantified and used to provide a range of design options and to quantify the level of risk in selected design outcomes. / Ph. D.

Many passive margins experience pulsed exhumation events late in their history as a result of plate boundary distal geodynamic mechanisms or climatic events. The onset of late Cenozoic glaciation, often associated with enhanced rates of erosion, is one such possible cause of passive margin rejuvenation. However, along passive margins the effectiveness of Plio-Pleistocene glaciers at eroding the landscape may be limited by low tectonic rock uplift rates or as a result of erosionally inefficient cold based continental ice-sheets. In this dissertation the evolution of post-orogenic topography and the effect of glaciations on denuding landscapes along the North Atlantic Passive Margin, in the White Mountains of New Hampshire and the western Scottish Highlands, was investigated. Background exhumation rates averaged over 106-7 yr timescale were determined using apatite (U-Th)/He thermochronology. To resolve whether or not a change in exhumation rate occurred coincident with glaciation these background exhumation rates were compared to magnitudes of erosion averaged over the glacially relevant 103-4 yr timescale using the in situ terrestrial cosmogenic nuclide 10Be. In chapter two, 106-7 yr timescale exhumation and burial histories across the western Scottish Highlands were determined. The results show that post-orogenic burial and exhumation is mostly a result of plate margin distal tectonic and magmatic factors that are variable across short distances (i.e., <100 km). In chapter three, patterns and magnitudes of erosion during glaciation and following deglaciation in the Scottish Highlands were investigated. The results indicate that polythermal glacial erosion denuded low elevation portions of the Scottish Highlands and preserved summits. This produced relief but did not significantly lower the maximum elevation of the landscape. Following deglaciation Scotland's sediment budget remains dominated by glaciogenic sediment. In the fourth chapter, magnitudes of background exhumation in the Presidential and Carter Ranges of the White Mountains, New Hampshire were compared to magnitudes of glacial erosion. The results indicate that most relief was produced prior to glaciation and that background exhumation rates in the Cenozoic are low (<0.01 mm yr-1). In the late-Cenozoic, cold- based glaciation prevented an acceleration of erosion in the White Mountains. The post- glacial sediment budget is made up of dominantly glaciogenic sediment. Overall, the main findings of this dissertation are; (1) post-orogenic burial, exhumation, and relief production are mainly the result of spatially heterogeneous plate margin distal vertical crustal motions; across passive margins covered by large continental ice sheets; (2) cold-based ice limits the magnitudes of late Cenozoic glacial erosion sediment budgets continue to be dominated by glaciogenic sediment, >10 ka after and (3) post-glacial deglaciation. / Ph. D.

According to the Mine Health and Safety Administration (MSHA), between 2006 and 2016, the underground stone mining industry had the highest fatality rate in 4 out of 10 years, compared to any other type of mining in the United States. Additionally, the National Institute for Occupational Safety and Health (NIOSH) stated that structurally controlled instability is a predominant failure mechanism in underground limestone mines. This type of instability occurs when the different discontinuity sets intercept with each other forming rock blocks that displace inwards the tunnel as the excavation takes place, posing a great hazard for miners and overall mine planning. In recent years, Terrestrial laser scanning (TLS) has been used for mapping and characterizing fractures present in a rock mass. TLS is a technology that allows to generate a three-dimensional multimillion point cloud of a scanned area. In addition to this, the advances in computing power throughout the past years, have allowed numerical modeling codes to represent more realistically the behavior of a fractured rock masses. This work presents and implements a methodology that integrates laser scanning technology along with Discrete Element Modeling as tools for characterizing, preventing, and managing structurally controlled instability that may affect large-opening underground mines. The stability of an underground limestone mine that extracts a dipping ore body with a room and pillar (and eventual stoping) mining method is analyzed with this approach. While this methodology is proposed based on a specific case study that does not meet the requirements to be designed with current NIOSH published guidelines, this process proposes a general methodology that can be applied in any mine experiencing similar failure mechanisms, considering site-specific conditions. The aim of this study is to ensure the safety of mine workers and to reduce accidents that arise from ground control issues. The results obtained from this methodology allowed us to generate Probability Density Functions to estimate the probability of rock fall in the excavations. These models were also validated by comparing the numerical model results with those obtained from the laser scans. / M.S. / According to the Mine Health and Safety Administration (MSHA), between 2006 and 2016, the underground stone mining industry had the highest fatality rate in 4 out of 10 years, compared to any other type of mining in the United States. Additionally, the National Institute for Occupational Safety and Health (NIOSH) stated that structurally controlled instability is one of the main causes of rock falls in underground limestone mines. This type of instability occurs when the fractures present in the rock mass intercept each other forming rock blocks that displace into the tunnel as the excavation takes place and poses a great hazard for miners. In recent years, Terrestrial laser scanning (TLS) has been used for mapping and characterizing fractures present in a rock mass. TLS is a technology that allows to generate a three-dimensional multimillion point cloud of a scanned area. In addition to this, the advances in computing power throughout the past years, have allowed simulation softwares such as the Discrete Element Model (DEM) to represent more realistically the behavior of a fractured rock mass under excavation. The aim of this work was to develop and evaluate a methodology that could complement already exisiting design guidelines that may not apply to all kind of underground mines. The presented methodology evaluates rock failure due to presence of discontinuites, through the integration of TLS with DEM and considers site specific conditions. An area of a case study mine was assessed with this methodology, where several laser scans were performed. Information extracted from this laser scans was used to simulate the response of the rock mass under excavation by running Discrete Element Numerical Models. Results from these models allowed us to estimate the probability of rock failure in the analized areas. These, rock block failure probability estimations provide engineers a tool for characterizing, preventing, and managing structurally controlled instability, and ultimately improving workers safety.