A 12-month study (January to December 2015) focused on the effects of tidal forcing on nutrient fluxes in the tidal, freshwater segment of the James River Estuary (JRE). Discrete sampling of nutrient chemistry and continuous monitoring of tidal discharge were used to determine the volume and timing of the tides, and differences in nutrient concentrations between incoming and outgoing tides. The goal of this study was to improve understanding of tidal influence on nutrient fluxes and their role in nutrient transport to the lower estuary. Results suggested that differences in nutrient concentrations between incoming and outgoing tides were small throughout the year. This finding suggests that nutrient fluxes at the study site, near the tidal fresh-oligohaline boundary of the James, are largely determined by tidal volume owing to weak concentrations gradients. Changes in water quality during seaward and landward tidal excursions into deeper versus shallower segments were analyzed to infer biogeochemical processes. Differences in oxygen production and nitrate utilization suggest greater autotrophy during landward excursions, consistent with more favorable light conditions. This work was conducted as a collaborative effort between Virginia Commonwealth University, the USGS, Randolph-Macon College, and Washington and Lee University participating in the “Mountains to the Sea” project.

Anecdotal evidence suggested that immature lemon sharks (Negaprion brevirostris) occur at the Chandeleur Islands in southeastern Louisiana. From May 2009 to August 2011, the Nekton Research Laboratory at the University of New Orleans regularly sampled habitats at the Chandeleur Islands to confirm the presence of immature individuals of this species. During these efforts, 147 immature lemon sharks (neonates, young-of-the-year, and juveniles) were collected. Each shark was PIT tagged and a tissue sample was taken for genetic analyses. Sizes ranged from 56 – 177 cm total length. Sharks showed a preference for sandy substrate and smaller individuals showed significant preference for shallow waters. Collection data for N. brevirostris were obtained from various locations around the Gulf of Mexico for comparison. Based on a review of current literature, collection data, and microsatellite analysis it was possible to classify the Chandeleur Islands as an elasmobranch nursery ground under the definition presented by Huepel et al. (2007). Current literature and high densities of N. brevirostris suggests that the Chandeleur Islands are the only area in the northern Gulf of Mexico where neonatal and YOY lemon sharks have been recorded. Results from a combination of SPOT 5 satellite tags, PIT tags, and FLOY tags show that immature N. brevirostris at the Chandeleur Islands remain in the vicinity of the islands for several months. The abundance of juvenile sharks across years provides evidence of continuous use of these islands as a pupping area. Genetic analysis supports this information with 7 of 15 mothers returning across years. The combination of this information indicates that the Chandeleur Islands are the northern- and western-most documented nursery ground for this species. Special care should be given to this habitat as CPUE for N. brevirostris decreased significantly during this research following the 2010 Deepwater Horizon disaster and subsequent oil prevention measures. Genetic research indicates a high level of inbreeding and genetic separation between the Chandeleur Islands population and other known populations in Florida, Belize, and the Bahamas.

Studies were conducted on a population of tiger salamanders, Ambystoma tigrinum, at Henderson Island Wildlife Management Area in Jefferson County, TN. Tests were conducted to locate the nonbreeding habitat of the salamanders and to detect any difference in fluctuating asymmetry (FA) between larval populations in a large, permanent pond and an ephemeral wetland. Drift fences were installed with pitfall traps at selected locations around each pond to determine nonbreeding habitat use by adults. Most adult salamanders were found using a blackberry (Rubus sp.) dominated old-field, a grassy field, and a shrub-grass mix field, which were all adjacent to the ponds. No statistical difference in FA between the 2 ponds.

The Asian clam, Corbicula fluminea, is an invasive bivalve species that now occurs through most of the lower 48 United States. While a significant degree of salinity tolerance has been observed in C. fluminea, owing to its estuarine lineage, the physiological and behavioral responses to changes in salinity by these organisms are not completely understood. It was hypothesized that Corbicula would initially avoid elevated salinity levels (>1 g/L) behaviorally through valve closure, but would eventually have to open to dispel anaerobic waste products and deal with the salinity. To explore this, Corbicula were collected and put through a series of experiments at salinity exposures of 0, 2.5, and 5.0 g/L, with tissue water content and hemolymph osmolality being measured. After an initial 96-hour exposure, it was observed that the percent tissue water content of clams in 2.5 g/L and 5.0 g/L water dropped 3.29% and 4.18%, respectively, below that of the control groups in 0 g/L. After a 24-hour time-course experiment, this change in tissue water was found to largely occur within the first eight hours of exposure for the 2.5 g/L and 5.0 g/L groups. It was also noted that the hemolymph osmolality of both the 2.5 g/L and 5.0 g/L groups rose to approximately 78 mOsm/kg and 148 mOsm/kg, respectively, matching the osmolality of their exposure water in roughly the same time span and indicating that little behavioral avoidance of the elevated salinity was occurring. The osmolality of the control group did not match the osmolality of the 0 g/L water at 0.5 mOsm/kg, but was held at a constant level around 50 mOsm/kg. In a later experiment measuring the same variables for clams in 10.0 g/L, it was found that the tissue water and osmolality did not begin to change significantly until after 12 hours, indicating behavioral avoidance at this salinity level. A context study was also conducted comparing oxygen consumption and percent tissue water between various salinities in a light and dark exposure to determine if ambient light influenced siphoning of the clams and exposure to the salt. In this experiment, it was observed that clams held in salinities of 5.0 g/L for 24 hours consumed roughly 1.90 mg O2/L/g/h, whereas clams held in the control only consumed roughly 0.73 mg O2/L/g/h. These findings suggest that Corbicula osmoregulate in freshwater but osmoconform at salinities of 2.5 g/L and 5.0 g/L. The data from the context study also suggests that this conformation comes at a significant metabolic cost. Furthermore, and in contrast to the results of some previous studies, a significant level of behavioral avoidance of elevated salinity does not appear to commence until the clams are at a salinity above 5 g/L.

Large scale ecosystem restoration is an important societal issue because significant risks, costs, and benefits can accrue on large landscapes. It is important to understand baseline ecosystem conditions, existing condition, and to the extent possible estimate ecosystem response to alternative management scenarios. Incorporating ecosystem process and function into restoration planning and implementation will make ecosystem restoration projects sustainable. The Upper Mississippi River System is an excellent case study for such issues because it is an important, multiple-use ecosystem with significant ongoing investment in ecosystem, agri-system, and navigation system management. Large-scale geomorphology, hydrology, and land cover information was compared among presettlement, contemporary, and potential future reference conditions to examine ecosystem state and evaluate mechanisms responsible for ecosystem condition. The UMRS was scaled by physiographically similar characteristics into large floodplain reaches several hundred river miles in length, geomorphic reaches 50 to several hundred miles, and a mile-by-mile segmentation of the river floodplain extent. Ecologically relevant geomorphic classes were devised from existing data and evaluated by river reach to characterize presettlement geomorphology, and dams and levees were superimposed to reflect the altered hydrogeomorphology of the contemporary ecosystem. A pre- and post-impact Indicators of Hydrologic Alteration river stage analysis evaluated dam impacts, and pre-dam and post-dam aquatic habitat class distribution was compared. A floodplain inundation simulation analysis provided new information on the potential spatial distribution of frequent floods. Land cover data available for presettlement and modern reference periods were compared at several spatial scales. Multivariate analyses evaluated land cover characteristics among geomorphic reaches, as well as to assess the influence of hydrogeomorphic drivers on land cover for presettlement and contemporary reference periods. The objective of this research was to clearly delineate the divergence of environmental conditions among reference periods to evaluate which drivers need to be, and can be, altered to change ecosystem state. Hydrogeomorphic response to development indicates several restoration objectives that are appropriate system-wide and others that are best suited to specific river reaches. Similar data sources are available for much of the rest of the United States through the Public Land Survey and engineering surveys of any significant civil works projects.

The Bonneville Power Administration (BPA) Fish and Wildlife Program mitigates for impacts of hydroelectric dams on ESA-listed salmon and steelhead populations in the Columbia River Basin (CRB). Considering the sizable investments in mitigation and the diversity of stream habitats within the CRB, there has been a pointed effort to develop and identify meaningful metrics relating to fish populations and trends in their habitat across the CRB. The Integrated Status and Effectiveness Monitoring Program (ISEMP) was developed in 2003 specifically for this purpose, and is tasked with developing and testing strategies for determining the status and trend of salmonid populations and their habitats in the CRB. This thesis was funded by the BPA, ISEMP, Eco Logical Research Inc., the Snake River Salmon Recovery Board, and the Intensively Monitored Watershed project in the Asotin Creek basin with the purpose of investigating the efficacy of foraging modeling as part of a large fish habitat monitoring program. The primary objectives were i) to assess a foraging model's ability to predict fish density in study sites involved in long-term monitoring and ii) to evaluate energetic implications of restoration design and progress after implementation using a foraging model. To assess the foraging model's ability to predict fish density (objective i), we collected topography, drift, temperature, discharge, and fish population information to support foraging modeling, and we simulated flow patterns, drift, foraging, swimming costs, carrying capacity, and density. We then compared observed and predicted densities in 22 study sites from the John Day and Asotin Creek watersheds: Linear regression between observed and predicted fish densities was significant (R2 = 0.61, p < 0.001). When assuming spatially uniform drift densities and small fish territories, carrying capacity predictions were related to the number of foraging locations simulated, suggesting the model is highly sensitive to territory size assumptions. To evaluate restoration design and monitor restoration progress (objective ii), we simulated foraging before restoration, after a virtual restoration (carried out using the restoration designs in a GIS environment), and again followinfg restoration implementation. We used raster differencing to compare the "before" results to the virtual restoration results and then the "before" results to the "after" results. Hydraulic and foraging models suggested: Mean net energy intake increased following both simulated and actual restoration. Restoration structures generally slowed water's progress through the study site or caused pooling, both resulting in an increase in energetically favorable areas. Generally, more areas shifted from another state to having an acceptable energy balance than to an unacceptable energy balance.

There is currently a decline in large, old trees within many ecosystems where they play important ecological and economic roles. One ecosystem suffering from this decline is the bushveld savanna of South Africa. One particularly important species in decline is the ecologically, economically, and culturally significant marula tree (Sclerocarya birrea subsp. caffra). This species’ decline is characterized by a steep drop in recruitment of seedlings into the population. Rodents are known to influence plant communities across many ecosystems through herbivory of adult plants as well as predation of seeds and seedlings. This research provides a record of rodent species present in the bushveld savanna ecosystem of Balule Nature Reserve where a decline in marula recruitment is taking place. Further, it offers a summary of morphological statistics and natural history traits for these rodents. Morphological statistics can be used for species identification. Reproductive status of individuals can inform researchers about reproductive phenology and how it may be affected by environmental conditions. Finally, trapping for this study took place during an historic regional drought. Trapping success was used to develop a limited window into how reduced precipitation affects rodent abundances. Morphological traits measured coincide with those available in the literature. Reproductive activity for males and females of one species, Namaqua rock mouse (Micaelamys namaquensis ), did not overlap completely, with females not being reproductively active while males were. Individuals captured and identified as chestnut climbing mice (Dendromus mystacalis) had statistically significantly longer tails and hind feet, and were heavier than reported in reference works.

Pathogenic fungi are increasingly associated with epidemics in wildlife populations and represent a significant threat to global biodiversity. Snake fungal disease is an emerging disease caused by the fungus, Ophidiomyces ophiodiicola, and appears to be widespread in the eastern United States. Yet an evaluation of field diagnostics, and an understanding of the population-level consequences of the disease, are lacking. First, I evaluated the use of clinical signs to predict the presence of O. ophiodiicola across season and snake habitat affiliation (aquatic or terrestrial) and I compared two sampling methods to see if collection method impacts PCR result. Overall, snakes with clinical signs had a higher probability of testing positive regardless of season or habitat association. However, terrestrial snakes had a lower overall probability of testing positive for O. ophiodiicola compared to aquatic snakes. I found no significant difference between sampling methods. Second, I used Passive Integrated Transponder (PIT) telemetry, and multistate capture-mark-recapture modelling to determine if SFD affects the short-term survival, movement, and behavior of wild snakes. I found no difference in short-term survival for snakes with SFD. Snakes with SFD spend more time surface-active and have lower permanent emigration and temporary immigration rates than snakes without SFD.

Rhinichthys osculus, the Speckled Dace, is one of the most ubiquitous fish in western North America. Within the Southern California region, the local taxon is known as the Santa Ana Speckled Dace. The purpose of this study was to characterize and identify polymorphic microsatellite markers for R. osculus in which twenty-three were identified through Illumina pair-end sequencing. Seven of these loci were then used to examine the patterns of genetic variation and population structure that occurred within and among the watersheds in the Southern California. The study also examined the regional relationships among Southern California, Central California and Owen’s River Valley. Analysis of the microsatellite data revealed highly significant moderate levels of population structure exist within the Southern California region (RST=0.160, p=0.001). This structure is best explained by watershed as well as isolation by distance (R2=.2286, p=0.010). Highly significant geographic structure also exists among the geographic regions of Southern California, Central Coast, and Owen’s River Valley regions (RST= 0.600, p-value=0.001) that are congruent with the regional differentiation elucidated by mtDNA sequence data. In both cases, the degree of population differentiation was correlated with isolation by distance. Utilizing this information we were able gain a better understanding of the evolutionary relationships among the Southern California populations of Santa Ana Speckled Dace. Within the Santa Ana Speckled Dace populations we examined four models to explain the geographic structure: watershed, mountain range, tributary, and isolation by distance. While all were significant, the tributary model exhibited the higher level of population structure (RST= 0.160, p-value=0.001) and a significant correlation was exhibited between geographic distance and population structure, suggesting isolation by distance may be playing a role. The results of the microsatellite analysis are congruent with an earlier broad scale analysis of mtDNA sequence data that suggests the Central California and the Owens Valley populations diverged from each other prior to the divergence of the Santa Ana Speckled Dace populations from the Colorado Basin populations, and that the Central Coast populations were not established as a result of a migration event from the Southern California populations, as was previously hypothesized. Primarily due to human activity, Santa Ana Speckled Dace habitat has become highly fragmented resulting in some populations becoming extirpated. We hope this study will guide the strategies for the conservation of the remaining populations of Santa Ana Speckled Dace and watershed management in Southern California.

‘Aigarchaeota’, a deeply branching lineage in the domain Archaea with no cultivated representatives, includes both thermophilic and hyperthermophilic microorganisms that reside in terrestrial and marine geothermal environments. The ‘Aigarchaeota’ consists of at least nine proposed genus-level groups that have been confirmed via 16S rRNA sequencing, with ‘Aigarchaeota’ Group 1 (AigG1) being the focus of this study. Based on cultivation-independent genomic data available from several AigG1 members in Great Boiling Spring (GBS), NV, and Yellowstone National Park, 22 different types of growth media were designed and tested for their ability to support growth of AigG1. One of these cultures, G1-10, was found to contain AigG1 at ~5% abundance, as well as other novel thermophilic microbial groups including a new species of the genus Pyrobaculum, members of the candidate phyla ‘Calescamentes’ and ‘Fervidibacteria’, and the novel archaeal lineage NAG1 (‘Geoarchaeota’). To attempt to obtain pure cultures of AigG1 and other novel thermophiles, a single-cell sorting system using an optical trap and a microfluidic device was constructed. The system was validated by sorting E. coli cells, which demonstrated that single, viable cells could be reliably obtained. Using this single cell sorting device on the G1-10 culture, a pure culture of a member of the genus Pyrobaculum was obtained, which was shown to represent a distinct species in this phylum by whole genome sequencing and in silico DNA-DNA hybridization. Additionally, a pure culture of the first representative of the candidate phylum ‘Fervidibacteria’ from an enrichment culture derived from G1-10. Additionally, to aid in morphology-based sorting of AigG1 and stable isotope labeling studies, fluorescence in situ hybridization (FISH) based on catalyzed reporter deposition (CARD-FISH) were developed and an AigG1-specific probe was tested. CARD-FISH was successfully used to detect AigG1 in both the G1-10 culture and in natural sediment samples from GBS. Stable isotope labeling incubations were performed with a variety of 13C-labeled substrates (bicarbonate, amino acids, sugars, and short chain fatty acids) on GBS sediments and G1-10 culture samples, and CARD-FISH was used to specifically detect AigG1 in the fixed samples. Nanometer-scale secondary-ion mass spectrometry (nano-SIMS) will then be used to determine whether AigG1 was capable of taking up the different carbon substrates tested. Overall, the results and accomplishments from this project and follow up nano-SIMS analysis will allow a better understanding of the metabolic potential of AigG1 and will aid future efforts to attempt to obtain pure cultures of this novel lineage.