This study combined documentation of four boat propeller scar types in Halodule wrightii seagrass beds in Mosquito Lagoon, Florida with manipulative field experiments to document scar recovery times with and without restoration. Scar types ranged from the most severe scar type (Type 1) with trench formation which had no roots or shoots in the trench, to the least severe (Type 4) scars that had no depth, intact roots and shoots shorter than the surrounding canopy. For 110 measured existing scars, the frequency of each scar type was 56% for Type 1, 10% for Type 2, 7% for Type 3, and 27% for Type 4. In the first manipulative experiment, experimental scars were created to document the natural recovery time of H. wrightii for each scar severity within one year. Type 4 scars recovered to the control shoot density at 2 months, while Types 1, 2, and 3 scars did not fully recover in one year. Mean estimated recovery for H. wrightii is expected in 25 months for Type 1, and 19 months for Types 2 and 3. For the second manipulative experiment, three restoration methods were tested on the Type 1 scars over a 1 year period. Restoration methods included: (1) planting H. wrightii in the scar trench, (2) filling the trench with sand, and (3) filling with sand plus planting H. wrightii. There was complete mortality of all transplants at 2 months and only 25% of scars retained fill sand after 1 year. With dense adjacent seagrass beds, natural recovery was more successful than any of my restoration attempts. Thus, I suggest that managers should concentrate on preventing seagrass destruction rather than restoration.

Microorganisms are key players in the ecosystem functioning. In this thesis, we developed a framework to preprocess raw microbiome data, build a correlation network, and analyze co-occurrence patterns between microbes. We then applied this framework to a marine microbiome dataset. The dataset used in this study comes from a year-long time-series to characterize the microbial communities in our coastal waters off the Cal Poly Pier. In analyzing this dataset, we were able to observe and confirm previously discovered patterns of interactions and generate hypotheses about new patterns. The analysis of co-occurrences between prokaryotic and eukaryotic taxa is relatively novel and can provide new insight into how marine microbial communites are structured and interact.

Throughout the world, birds represent the primary type of wildlife that people experience on a daily basis. However, a growing body of evidence suggests that alterations to the acoustic environment can negatively affect birds as well as humans in a variety of ways, and altered acoustics from noise pollution has the potential to influence human interactions with wild birds. In this thesis, I investigated how anthropogenic noise impacts daily behavior as well as community structure of wild birds. In the first component of this thesis, I assessed the distance at which a bird initiates flight or escape behavior (i.e., flight initiation distance or FID) in varying acoustic conditions. I surveyed 12 songbird species from three foraging guilds, ground foragers, canopy gleaners, and hawking flycatchers, and I predicted FIDs to decrease, remain the same, and increase with noise exposure, respectively. Contrary to expectations, the canopy gleaning and flycatching guilds exhibited mixed responses, with some species exhibiting unchanged FIDs with noise while others exhibited increased FIDs with noise. However, FIDs of all ground foraging species and one canopy gleaner decreased with noise levels. In the second component, I examined the feeding of wild birds, an increasingly popular recreational activity throughout North America that promotes increased sense of wellbeing by connecting people with wildlife and nature. I tested how experimental noise influences abundance, species richness, community structure and foraging behavior of songbirds at maintained bird feeders. By measuring activity levels of all species that utilized the feeders exposed to intervals of quiet and noisy conditions, I found noise to be a significant predictor of community turnover. Specifically, noise exposure resulted in increased feeder activity for two species, and decreased activity for one species. I also confirmed previous research conducted in the laboratory indicating white-crowned sparrows decrease their foraging rate under noise conditions, presumably as a trade off with visual vigilance. Considering the interactions of humans and wild birds, the results from my two thesis components indicate that the acoustic environment can play a role in how species of different foraging guilds respond to birdwatchers and what species visit bird feeders.

The arroyo toad (Anaxyrus californicus) is a federally endangered species found on Fort Hunter Liggett, Monterey County, California. The species was discovered in 1996 and was determined to occupy 26.7 km of the San Antonio River from approximately 2.4 km northwest of the San Antonio Mission de Padua, to the river delta above the San Antonio Reservoir. The construction of the San Antonio Reservoir dam in 1963 isolated this northern population of arroyo toads. Through time, the Fort Hunter Liggett landscape has changed drastically. The land was heavily grazed by cattle until 1991, which considerably reduced vegetation in riparian areas. Military training following acquisition of the land in 1940 far exceeded current allowable training. Fire was used extensively to reduce unfavorable vegetation, and as a result, extreme tree loss occurred through the ranges. Today cattle grazing is prohibited and military activity is restricted from riparian corridors. While riparian vegetation continues to recover in the San Antonio River, habitat for breeding arroyo toads has become less suitable. To improve conservation efforts and management of this endangered species, I have provided a thorough assessment of the life history of arroyo toads specific to Fort Hunter Liggett and identified the status and current threats to the population on the installation. I have also prepared a habitat assessment of the San Antonio River in the arroyo toad range, quantified habitat conversion, and identified areas that may no longer provide suitable breeding habitat for the species. The research conducted for this report is preliminary to restoration efforts that are inevitable to ensure recovery of the endangered species at Fort Hunter Liggett.

Cephalopods provide forage to a wide range of predators in marine food-webs. Despite their ecological importance, a basic understanding of the mechanisms controlling predation risk and demand is lacking. This is true of one of the most common species of squid found in the northwest Atlantic, the longfin inshore squid (Loligo pealeii). In this dissertation, I address this shortcoming by investigating the role that size and behavior play in influencing squid’s vulnerability to predation. I used long-term food habits, population survey, and commercial landings data, to quantify size-based patterns of predation respective to 25 species of predators. Additionally, I estimated the amount of overlap between predatory consumption and the fishery catch for squid by size. I found that finfish and elasmobranchs generally consumed juvenile and sub-adult squid, while marine mammals primarily targeted adults. Consequently, marine mammals had the highest overlap with the fishing industry for squid size resources. Although large squid were not common in predator diets, predators did not appear to be gape-limited when feeding on squid. This suggested that other factors, including behavior, were important in shaping size-based patterns of predation. I used a laboratory-based approach to quantify attack and capture behaviors towards squid by two predators representing contrasting foraging tactics. Bluefish (Pomatomus saltatrix) and summer flounder (Paralichthys dentatus) were chosen as cruising and ambush predators, respectively. Patterns in attack rates suggested that sizeselection on squid was constrained by passive processes rather than active choice in both predators. Size-dependent profitability functions were calculated by combining capture success rates, handling times, and relative prey mass, and determined that bluefish was the more efficient predator of squid. Lastly, I evaluated the occurrence and effectiveness of anti-predator responses used by squid in the presence of bluefish and flounder. Squid behavior depended on the type of predator present, and the survival value of primary and secondary defense behaviors differed during interactions with each predator. The results of this project are intended to improve the quality of management of squid and their predators by providing a better understanding of predator-prey interactions in the northwest Atlantic.

A comparative study of the field populations of Crepidula lingulata, Crepidula nurnmaria, and Calyptraea fastigiata indicated all three preferred a rocky substrate but favored different size rocks. Their positions on the rocks varied but the greatest numbers were found attached to the undersides. Crepidula lingulata and C. nummaria preferred larger rocks and were found in intraspecific associations more often than C. fastigiata which preferred smaller rocks. These associations occurred with a 1:1 sex ratio; however, the overall population did not. Crepidula lingulata had a high female count and C. fastigiata a high male count. Males, of all three species, were smaller in size than females. Leptasterias hexactis and Evasterias troschellii were found to be possible predators. Protection was afforded those attached to the undersides of rocks. All three species used the radula to remove irritants from under the shell including the tube feet of attacking sea stars.

Three heteromyid rodent species were studied in relation to a large dry wash in Millard County, Utah, during the summer, 1974. Data were gathered with three trapping grids and analyzed to determine if the dry wash influenced rodent movement and distribution patterns. Dipodomys ordii and Dipodomys microps were distributed non-randomly in the dry wash and adjacent habitat, but Perognathus Zongimembris seemed to be randomly distributed. Dipodomys ordii was significantly correlated with wash habitat, but D. microps was found most frequently in upland areas. Soil and vegetative differences and competition were possible causes for the observed distribution. The wash was observed as a source of dispersing young D. ordii. It was concluded that the dry wash had little effect on daily movement of the rodents observed.

The adequacy of the negative exponential model with one independent variable, days or accumulated time, as a descriptive equation for aquatic leaf litter processing was examined. The effect of adding a second independent variable, degree days or accumulated temperature, to the model was also examined. The two variable negative exponential model was shown to have at least two advantages over the single variable model. The two variable model adequately fits litter processing data for more cases than the single variable model. The expanded model also allows determination of rate coefficients for various temperature levels of the experiment rather than assuming a single, constant rate coefficient as the simpler model does. The trends of the temperature dependent rate coefficient can be used to examine processing differences between experiments for different sites and seasons.

The upper water column (<1 m depth) of freshwater lakes, which includes the surface microlayer (SML; <1 mm depth), is an important microbial habitat as well as an accumulation and dissemination site for chemical and microbial contaminants. This doctoral thesis reports novel insights into how the physical structure and functional capabilities of microbial communities can influence the presence of trace metals and health-relevant bacteria in the upper waters (SML and 0.5 m depth) of freshwater lakes. Two physically and geochemically contrasting lake environments, a remote sheltered boreal lake and a higher energy urban beach on Lake Ontario, were investigated to identify system-dependent physical and biogeochemical factors controlling contaminant-relevant microbial characteristics. The SML was identified as a major site for generation of contaminant-sequestering suspended flocs from a distinct biofilm-forming microbial community over diurnal timeframes via wind and sunlight exposure, with this process being enhanced at the higher energy beach site. More generally, upper waters including the SML were demonstrated to be inhabited by a diverse group of atypical facultative Fe(III)-reducing bacteria (IRB) that exhibited a SML- and lake-specific capacity for solid Fe(III) reduction directly related to floc and Fe(III) availability. Although IRB were hypothesized to be highly resistant to metals and antibiotics relative to other bacteria due to their ability to dissolve metal-rich Fe(III) minerals, this was not found to be the case. Nevertheless, IRB enriched from the SML demonstrated higher antibiotic resistance compared to those from 0.5 m depth and enriched Fe(III)-reducing communities from both depths harboured resistance-mobilizing genetic elements and included potentially pathogenic bacteria. Results of this thesis represent new knowledge concerning how microbial communities regulate the presence of contaminants in the upper waters of lakes. This has important implications for assessing the ecological and human health impacts of contaminants in freshwater systems. / Thesis / Doctor of Philosophy (PhD)

Organisms are often exposed to multiple stressors in their natural habitat. While the effects of individual stressors alone are generally well-studied, their combined interactions are often unknown. One such unknown interaction is that between copper, an essential micronutrient that is toxic in high levels, and hypoxia, a commonly experienced environmental stressor. This project sought to examine the effects that copper has on the hypoxic response as well as the combined effects of copper and hypoxia exposure using freshwater-acclimated adult killifish (Fundulus heteroclitus), a model euryhaline teleost. It was found that copper blunts the acute ventilatory response to hypoxia, ammonia, and combined hypoxia and ammonia exposure. Gill morphometry was also examined and it was found that while copper alone has no effect, when combined with hypoxia exposure it eliminates the increase in filament length and cross-sectional area seen when fish were exposed to hypoxia alone. Furthermore, when neuroepithelial cell size was examined, copper decreased cell projection area with or without the combined presence of hypoxia. Taken as a whole, this thesis indicates that copper exposure can significantly and negatively impact the ability of aquatic organisms to mount appropriate physiological responses to hypoxia. / Thesis / Master of Science (MSc)