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Roadways are a pervasive feature of northeastern landscapes and can be a significant source of mortality for turtles. Until recently, little has been known about the design requirements for successful under-road passages for turtles and other wildlife to move safely between bisected habitat patches. At outdoor laboratories, using a factorial experimental design, we examined movements in response to varying light levels, and barrier opacity for painted turtles (Chrysemys picta, n=833), Blanding’s turtles (Emydoidea blandingii, n=49), and spotted turtles (Clemmys guttata, n=49). Additionally, we examined tunnel size, tunnel entrance design, and artificial lighting for painted turtles only. All three species responded poorly to a 0% available light treatment. As the amount of natural light transmitted through the tops of tunnels increased, successful completion of the trials increased. Furthermore, turtles generally moved at a slower rate when traveling along a translucent barrier, compared to an opaque one. Our results indicate the importance of designing road passage structures for freshwater turtles that provide adequate tunnel lighting in combination with specific entrance designs that meet the goals of the project.

Calcium stable isotope ratios are a relatively new tool that biogeochemists can use to investigate the biogeochemical cycle of calcium in terrestrial ecosystems, having seen widespread application only in the past 15 years. To advance the application of calcium isotopes in biogeoscience research, I conducted three investigations focused on interpreting calcium isotope ratios in streamwater and in the cation exchange pool of forest soils. In the first study, we observe a shift toward lower 44Ca/40Ca ratios in streamwater draining a New Hampshire watershed after an experimental clearcutting event. Isotope ratio measurements of ecosystem calcium pools indicate that enhanced leaching of the soil exchangeable pool produced the observed shift in 44Ca/40Ca ratios. A trend towards decreased 44Ca/40Ca ratios in soils in the years following the harvesting indicates that calcium leached from the soil exchangeable reservoir was likely replaced by calcium released by the decay of belowground biomass, maintaining pre-harvest levels of exchangeable calcium even in the face of a significant ecosystem disturbance. In a second study, we observed significant differences in the 44Ca/40Ca of the soil exchange pool between two neighboring tropical watersheds, although 44Ca/40Ca of calcium inputs (bedrock and atmospheric deposition) at the two sites were indistinguishable. Further, both sites had higher 44Ca/40Ca ratios compared with external inputs, a relatively rare observation globally. We propose that hurricane disturbance best explains the high 44Ca/40Ca at each site, and that the difference in 44Ca/40Ca between the two sites can be accounted for by the magnitude of disturbance at each site. Finally, a synthesis of our new data with previously published results shows that globally, soil exchangeable 44Ca/40Ca ratios can be higher, lower or equal to external inputs. Modeling work indicates that in addition to isotopic fractionation, the balance in fluxes between vegetation and soil is critical in determining how soil exchangeable 44Ca/40Ca ratios vary relative to external inputs. When plant uptake and return to the soil are equal, soil and external inputs 44Ca/40Ca are equal, while high soil 44Ca/40Ca ratios develop when uptake exceeds return. Soil develops low 44Ca/40Ca when biomass obtains calcium from sources other than the exchangeable reservoir.

A seasonal survey of the distribution of terrestrial tardigrades on Dugger Mountain, Alabama, was conducted during the time period from April 1997 through April 1998. Cryptogams from five trees (Quercus alba), three on north-facing slopes and two on south-facing slopes, were sampled seasonally at three stations (645 m, 410 m, 183 m) along an unnamed tributary of the South Fork of Terrapin Creek. Trees were chosen based on their location outside the riparian zone. Tardigrades were extracted from the samples, mounted individually in Hoyer's medium, and identified to species with phase microscopy. Seasonal and altitudinal variations in the distribution of the populations on the north- and south-facing slopes were determined. Present on Dugger Mountain were tardigrades belonging to 12 species (Macrobiotus cf. areolatus/tonollii, Macrobiotus cf. echinogenitus, Macrobiotus islandicus, Macrobiotus richtersi, Minibiotus intermedius, Milnesium tardigradum, Diphascon pingue, Hypsibius pallidus, Echiniscus cf. arctomys. Echiniscus virginicus, Pseudechiniscus ramazzottii, and Pseudechiniscus suillus). Due to the small numbers of individuals of each species, the total numbers of tardigrades of all species were pooled. There were no significant differences in the mean number of species or the mean number of all tardigrades per sample at each station (altitude). However, seasonal differences in both abundance and number of species were detected in pooled samples due to the high numbers collected in spring 1997.

The objectives were (1) to relate terrestrial vertebrate responses to the management practices used for lodgepole pine forests within the Barometer Watershed, Mountain View Ranger District, Wasatch National Forest, Utah . (2) To correlate terrestrial vertebrate densities or frequencies with community types, edge, major forest stand structures , and (3) to propose management plans to manipulate densities of major vertebrate species in a predetermined manner. The study was conducted between 1973-1975 and provides a detailed description of forest vegetation for 53 lodgepole pine (Pinus contorta) stands. For each of these stands, a complete summary is provided of tree populations, coverage, and frequency of major vascular undergrowth species . Eight lodgepole pine forest community types are defined. A key is provided for identification of each community type and its anticipated habitat type. The relationships between densities of major vertebrate species, forest communities, and major forest stand structures are described. Big game utilization of ecotones created by mountain meadows and the lodgepole pine forest are discussed. In addition, the response of selected small mammal and big game species to clearcut size is provided. Important research findings were: (1) In the lodgepole pine forest most vertebrates exhibit preferences for specific community types. (2) Due to the broad definition of present habitat classifications, limited predictions can be made about the general response of wildlife populations on most sites. (3) The use of park-like openings and associated peripheral timber hy big game animals is closely associated with community type, edge configuration, and historical travel lanes. (4) An abundance of downed woody material enhances big game calving and resting areas. (S) The number of bird species is closely associated with understory biomass and diversity. (6) Management schemes that speed up the rotation of lodgepole pine overstories eliminate certain vertebrate communities associated with the final successional stages. The following specific recommendations for overstory removal are suggested. (1) Timber sales should be developed by drainage, with longterm objectives that insure the distribution of a variety of communities within a drainage. (2) The addition of major stand structure information should be included in habitat classification systems. (3) Timber sales should be designed with irregular edges and buffers of standing timber which provide cover and concealment. (4) Moist sites and relic areas, representing the final stages of succession, should be planned into the overall drainage sale philosophy. {5) In relatively undisturbed areas, vehicular travel should be prohibited following overstory removal.

Any marsh is a distinctive land-forrm of varied interest. To the agriculturist it is wasteland to be reclaimed; to the naturalist, a habitat of aesthetic value. To the ecologist, however, a marsh represents a complexity of vegetation under the influences of many and often inseparable factors. It becomes a place of challenging study. There exists a notable lack of information treating the ecology of inland salt-marshes. Still less known are the ecological conditions imposed upon plant life in marshes arising from saline springs. The presence of such a wetland in western Utah afforded the opportunity to study salt-marsh vegetation in a highly specialized habitat. The study had two phases. First was a study of the vegetation. Data were secured from collections and study plots within each of the major marsh communities. General descriptions of other plant life were additionally compiled. It is not within the scope of this paper to discuss or rigidly define the requirements embraced in the use of "community" as a unit of vegetation. Sufficient references are available for those who wish to pursue the point. In this study, a community is a congregation of plants exhibiting differences in appearance and species composition from other plant congregations. Secondly, studies were directed to the influences of soil and water on the ecology of each community. Transects were used to investigate many of these relationships. Transition zones between communities were narrow and usually sharply delineated. Transects intersected ecotones of this sort; environmental differences which may have occurred in the few broader ecotones were assumed to be of equal magnitude but of more gradual rate of change . Relatively short transects thus adequately represented each community yet allowed collection of intensive data. Information and data were collected during a 5-week period in August and September 1959 and a 6-month period beginning in March 1960.

This thesis has two aims. The first one is the investigation and analysis of the errors occurring in the measurements with pulsed time-of-flight (TOF) terrestrial laser scanners (TLS). A good understanding of the error sources and the relationships between them is necessary to secure the data accuracy. We subdivide these errors into four groups: instrumental, object-related, environmental and methodological. Based on our studies and the results obtained by other researchers, we have compiled an error model for TLS, which is used to estimate the single-point coordinate accuracy of a point in the point cloud, transformed to the specified coordinate system. The second aim is to investigate systematic instrumental errors and performance of three pulsed TOF laser scanners – Callidus 1.1, Leica HDS 3000 and Leica HDS 2500 – and to develop calibration procedures that can be applied by the users to determine and correct the systematic errors in these instruments. The investigations have been performed at the indoor 3D calibration field established at KTH and outdoors. The systematic instrumental errors, or calibration parameters, have been estimated in a self-calibration according to the parametric least-squares adjustment in MATLAB®. The initial assumption was that the scanner instrumental errors are similar to those in a total station. The results have shown that the total station error model is applicable for TLS as a first approximation, but additional errors, specific to the scanner design, may appear. For example, we revealed a significant vertical scale error in the scanner Callidus 1.1, caused by the faults of the angular position sensor. The coordinate precision and accuracy of the scanners, estimated during the self-calibration, is at the level of several millimetres for Callidus 1.1 and Leica HDS 3000, and at the submillimetre level for Leica HDS 2500. In other investigations, we revealed a range drift of up to 3 mm during the first few hours of scanning, presumably due to the changes in the temperature inside the scanners. The angular precision depends on the scanner design (“panoramic” or “camera-like”), and the angular accuracy depends on the significant calibration parameters in the scanner. Investigations of the influence of surface reflectance on the range measurements have shown that the indoor illumination and surface wetness have no tangible influence on the results. The type of the material does not affect, in general, the ranging precision for Callidus 1.1, but it affects the ranging precision and accuracy of the scanners Leica HDS 3000 and Leica HDS 2500. The reason may be different wavelength and, possibly, different design of the electronics in the laser rangefinders. Materials with high reflectance and those painted with bright “warning” colours may introduce significant offsets into the measured ranges (5 – 15 cm), when scanned from close ranges at normal incidence with the scanner Leica HDS 3000. “Mixed pixels” at the object edge may introduce a range error of several centimetres, on the average, depending on the type of the material. This phenomenon leads also to the distortions of the object size, which may be reduced by the removal of the “mixed pixels” based on their intensity. The laser beam intensity recorded by the scanner tends to decrease with an increased incidence angle, although not as assumed by the popular Lambertian reflectance model. Investigations of the scanner Leica HDS 2500 outdoors have revealed no significant influence of the “normal” atmospheric conditions on the range measurements at the ranges of up to 50 m. Finally, we have developed and tested two simple procedures for the calibration of the vertical scale (and vertical index) error and zero error in laser scanners. We have also proposed an approach for the evaluation of the coordinate precision and accuracy in TLS based on the experiences from airborne laser scanning (ALS). / QC 20101123

In the Chesapeake Bay, < 1% of the historic oyster population remains, and efforts have been increasing to restore oysters and the services they provide. Building reefs that successfully provide ecosystem services–especially habitat and foraging grounds–may require different restoration techniques than those previously used, and success may depend on reef morphology (complexity), location, and environmental conditions. Salinity and habitat complexity are two important factors that may interact to effect benthic communities and predator-prey interactions on restored reefs. The goals of this project were: (1) Characterize the benthic communities on restored oyster reefs in lower Chesapeake Bay, and (2) examine the effects of structural complexity and salinity on benthic communities and predator-prey interactions. A two-year field survey of restored reefs was carried out in four rivers in lower Chesapeake Bay to characterize faunal communities on restored reefs and to quantify the effect of reef complexity on faunal communities. A laboratory mesocosm experiment was conducted to examine the effect of reef complexity on predator foraging. In total, 61 macrofaunal species were identified among all samples, and restored reefs supported on average, 6,169 org/m2 and 67.88 g-AFDW/m2. There were significant differences in the community composition and diversity among the rivers, and salinity was the environmental factor that best explained the observed differences in species composition across the rivers. Salinity and rugosity (i.e., structural complexity) both positively affected diversity, while salinity negatively affected macrofaunal abundance and biomass. Oyster density and rugosity positively affected macrofaunal biomass, and oyster density positively affected mud crab, polychaete, and mussel densities. In the mesocosm experiment, predator foraging, measured by proportion and number of prey consumed, was significantly reduced in the presence of oyster shell structure. However, predators were able to consume more prey when prey density was increased, even in the presence of oyster shell structure. These results combine to enhance our understanding of the benefits of increased habitat complexity for both prey and predators on restored oyster reefs. Increasing complexity worked to increase the abundance, biomass, and diversity of organisms inhabiting restored reefs, and even though predator consumption was reduced in the presence of structure compared to non-structured habitat, predators were able to consume more prey individuals when prey density was increased. Therefore, increasing the structure of oyster reef habitat may benefit prey species by providing refuge habitat, and benefit predators by providing an increased abundance of available prey items.

While deeper estuaries typically demonstrate predictable responses to increased nutrient loads, responses in shallow systems are more varied, due in part to the presence of multiple benthic autotrophs. Shallow systems are particularly vulnerable to increases in watershed nutrient loads due to their position at the interface between land and open water. The prevailing conceptual model of eutrophication for shallow systems currently describes a succession in the dominant autotroph from seagrass to macroalgae to phytoplankton, but this model does not include benthic microalgae, which can sequester nutrients in photic systems. The Virginia Eastern Shore is characterized by shallow lagoons connected to upland watersheds through small tidal creeks, where the main source of fresh water and nutrients is groundwater. While some studies have characterized the response of the lagoons to nutrient loads, little is known about the tidal creeks and whether they act as filters, transformers, or conduits for land-based nutrients. We examined the role tidal creeks play in modulating watershed nutrient inputs in the Great Machipongo River (GMR) system, the largest tidal creek complex on the seaside of the Virginia Eastern Shore. We developed a field monitoring program that provided data to calibrate a reduced complexity Estuarine Ecosystem Model (EEM). Production, respiration, and net ecosystem metabolism were quantified, using both the open water and component methods, seasonally at three sites within this system. These rates together with monthly concentrations of standing stock nutrients and water column chlorophyll, monthly DataFlow surveys of physiochemical parameters, seasonally and spatially-intensive benthic chlorophyll surveys, and a bathymetric survey were used to develop and calibrate the EEM. The model was used to assess the degree to which tidal creeks export (via flushing), remove (via denitrification), or transform (via autotrophic uptake) land-based nutrient loads to the adjacent lagoons during baseflow and storm conditions. Component metabolism studies showed the system was overall net autotrophic, with increasing dominance of benthic processes towards the head of the estuary. Open water metabolism studies suggested the system was overall net heterotrophic, but we believe this conclusion is biased by the surrounding marshes and violations of the constant water mass assumption. The creek system exported 61,476 kg N y-1 as phytoplankton biomass, an amount approximately equal to inputs from the watershed and atmosphere, and imported 172,830 kg N y-1 in dissolved inorganic forms for a net import of 111,354 kg N y-1 from Hog Island Bay. Phytoplankton uptake, benthic microalgal uptake, and denitrification accounted for 216%, 343%, and 38% of the annual input of watershed and atmospheric N to the system, indicative of rapid cycling and advection of nutrients from Hog Island Bay. The storm simulation showed that almost all of the additional 28,635 kg N y-1 added from the watershed was flushed to Hog Island Bay and a small portion was denitrified. This study indicates that GMR system function is dominated by benthic processes, and the system acts as a transformer and filter of land-based nutrients during normal conditions and a conduit of nutrients during storm conditions.

This thesis developed from the VIMS Larval Fish Monitoring Program, which began in 2007 as part of a study comparing the larval fish assemblages of Chesapeake and Delaware Bays. Ribeiro et al. (2015) analyzed data from the first three years of this time series to describe the temporal variation in the larval fish assemblages. After this initial study was completed (three years in duration), the sampling continued at the fixed station near the mouth of the York River, which was used to represent the Chesapeake Bay. For this thesis, therefore, eight years of data (2007-2015) were available to investigate temporal changes in the larval fish assemblage, and to better evaluate intra-annual variation of the larval fish assemblage. Further, larval fish indexes of five target species of commercial and recreational importance in the Chesapeake Bay, were examined, including Anchovy (Anchoa spp.), Atlantic Menhaden (Brevoortia tyrannus), American Eel (Anguilla rostrata), Summer Flounder (Paralichthys dentatus), and Atlantic Croaker (Micropogonias undulatus). Regression models were used to evaluate the effect of different environmental and temporal variables on the larval fish density from the York River system. Results show a stable assemblage in the York River since 2007, with marked seasonal patterns in terms of composition and abundance of larval fishes. The assemblage from May to August is formed by estuarine species with high number of larval fishes (e.g., Anchovy, Green Goby, Naked Goby); the assemblage from September to April is characterized by a lower number of species, mainly coastal spawners such as Atlantic Croaker, Summer Flounder, and Atlantic Menhaden. at the species level, slight annual variations were found, although in general abundances were stable across the time series. Because the larval fish monitoring program sampled at a single fixed station located in the lower portion of the York River system, it is limited spatially even though it has good temporal resolution (eight years). One fixed station may capture only localized patterns and it is unclear if this is comparable to the larval fish assemblage in southern portion of the Chesapeake Bay generally. The second chapter of this thesis addresses the question of spatial variation of the larval fish assemblage, principally between the York River system and the mouth of the Chesapeake Bay. Samples taken in three locations were compared to determine if the assemblage varied among the sampling locations. Larval stages of two coastal spawners, Atlantic Menhaden and Atlantic Croaker, were the two most abundant at both all locations. Results indicate species specific differences among the locations, for example, Atlantic Croaker larvae were more abundant in the York River mouth (YRM) than in the Chesapeake Bay mouth (CBM), indicating significant spatial variation in larval fish assemblage composition over a distance of approximately 40 km, the distance between the YRM and CBM. This variation should be taken into account when generalizing the structure of the larval fish assemblage of the York River spatially.