Introduction of fish species to North American drainages has occurred for over 100 years. Introduced fish species have been documented to have adverse effects on both the environment and native species of the drainage into which they have been introduced. To better understand the effects that introduced species may have on a particular drainage, it is essential to understand aspects of the introduced species’ life history. The objectives of the current study is to quantify the age, reproduction, growth, condition and diet of the yellow bass, Morone mississippiensis, in Barren River Lake, Kentucky. Monthly collections from three areas on Barren River Lake were made via a boat-mounted electrofisher from March 2008 to March 2009. Fish age was estimated by examining the sagittal otoliths of each individual. Reproductive condition was assessed using the mean gonadosomatic index (GSI) of all sexually mature individuals by month. Yearly growth rates were estimated by computing the mean length at age for each age class and subsequent calculation of the von Bertalanffy growth function (VBGF). To estimate the condition of yellow bass as it changed throughout the sample period, relative weight of each individual was calculated and the mean monthly relative weight was calculated. To examine the diet of yellow bass, diet items were identified to the lowest practical taxonomic level. Then, dry weight of each diet item was estimated and pooled by season to assess the season changes in the diet of yellow bass. Individuals of age group 3 were the most frequent. Mean GSI was significantly higher in March, April and May of 2008. Calculation of the VBGF yielded 254.7 mm as the maximum attainable mean total length of yellow bass in Barren River Lake. VBGF predicted mean total lengths of age classes 0-8 were as follows: 21.7 mm, 64.4 mm, 99.2 mm, 127.7 mm, 151.0 mm, 170.0 mm, 185.5 mm, 198.2 mm, and 208.5 mm. Relative weight was highest in summer. The diet of adult and sub-adult yellow bass relied heavily on chironomid larvae and pupae throughout the year, although diet item consumption was very low in winter. Young-of-year gizzard shad (Dorosoma cepedianum), however, became the most important adult diet item in the spring and summer. To better understand the impacts that the introduced yellow bass has on the ecosystem of Barren Rive Lake, a multi-year study including an estimation of relative abundance is recommended.

The blue crab, Callinectes sapidus, represents an ecologically and economically important component of marine and estuarine ecosystems. In Florida, blue crab landings accounted for $9.6 million dollars during the 2010 fishing season. Accurate stock assessments for this valuable fishery are essential. Age is a critical biological component of accurate stock assessments; however, blue crabs and other crustaceans are especially difficult to age because of the complex nature of discrete growth. Biochemical extraction of an aging pigment, lipofuscin, was developed using blue crab eyestalks. The current study investigated the effects of freezing preservation on lipofuscin extracts and examined whether the extraction methodology, developed by Chesapeake Bay researchers, was useful for aging Tampa Bay blue crabs populations. Significant differences in lipofuscin index were found between samples frozen (2 weeks at -80°C) prior to analysis and those processed and assayed immediately (p < 0.001). Quarterly assays of the cohort of known-age individuals revealed a negative linear trend (y = -0.12x + 0.49, p < 0.001) in lipofuscin index over a 12-month period. This result suggests that extraction of lipofuscin is not appropriate for age determination of Florida blue crabs. Investigations into possible causes of the negative trend in lipofuscin suggest this method deserves further examination and refinement before it is acceptable as a reliable method for age determination in Florida blue crabs. Growth data of the known-age population collected during this study revealed that blue crabs in Tampa Bay can reach exploitable size in under sixth months and female crabs can reach sexual maturity within seven months of hatching. These growth patterns have the potential to enhance future Florida stock assessments.

Recirculating aquaculture systems (RAS) produce aquaculture products on land with minimal discharge of waste products and minimal water loss. High costs associated with waste treatment for RAS have triggered the growth of integrated aquaculture systems (IAS) which incorporate macrophytes (aquatic plants) into the treatment train. The objective of this research was to examine a pilot scale inland marine IAS with three different methods for solids treatment: a sand filter followed by a plant bed, only a plant bed, and geotextile bags. Florida Pompano (Trachinotus carolinus) were grown along with Smooth Cordgrass (Spartina alterniflora), Black Needle Rush (Juncus romerianus), and Red Mangrove (Rhizophora mangle). Between May 2011 and April 2012, water quality was tested at seven points located throughout the IAS for total suspended solids (TSS), chemical oxygen demand (COD), total nitrogen (TN), ammonium (NH4+), nitrate (NO3-), total phosphorus (TP), and orthophosphate (PO43-) concentrations every 4 to 6 weeks. Plant and soil samples were collected three times and analyzed for total nitrogen and total phosphorus. A statistically significant difference in the effluent concentrations for the three treatments was not found; however, due to the recombination of effluent from the solid treatments and the variability inherent in a pilot scale system it was difficult to isolate the individual efficiencies of each treatment. Therefore, on average the complete system achieved COD and TSS removal efficiency of 59% and 88%, respectively and TN and TP removal efficiency of 48% and 19%, respectively. Nutrient uptake by plants did not vary significantly between the plant beds. In general, the system provided sufficient nutrient removal for safe fish production, and the fish provided enough nutrients for ample plant growth.

Freshwater mussels are the most imperiled group of freshwater invertebrates globally. Recent research suggests a better understanding of mussel feeding ecology may facilitate and improve conservation efforts. The use of stable isotopes is becoming an increasingly common method to study aquatic food webs. Carbon (C) and nitrogen (N) are two of the most frequently employed elements in food web studies. Differences in natural abundance of 13C/12C can indicate which food sources are the basal sources of carbon incorporated into a consumer’s tissue, while the ratio of 15N /14N provides a method of assessing trophic position within a food web. Attached macroalgae, including the genus Cladophora, may be the dominant primary producers in running water systems. Cladophora, however, has not yet been indicated as a prominent assimilated food source for freshwater mussels. The overall purpose of this study was to assess if the diet of two common Green River mussel species, Amblema plicata (Say) and Elliptio dilatata (Rafinesque) were influenced by the seasonal change in availability of Cladophora during a summer-autumn rapid growth period. Two specific questions were asked: 1) Are the assimilated diets different between control and treatment areas, and 2) are the assimilated diets influenced by differing Cladophora levels across the study period? A mesocosm approach was employed in order to manipulate Cladophora levels within a treatment area. Seventy-two mussels, 36 each species, were sampled across four months,twice between control (= reach-scale, heavy Cladophora cover) and treatment (= localscale removal of Cladophora) areas. The freeware program, IsoSource, a concentration weighted linear mixing model, was used to determine the potential contribution of potential food sources to the diet of both mussel species. IsoSource revealed that Cladophora was the primary assimilated food source for both species across the study period. Although assimilated diets were not different between control and treatment areas, diets were, however, influenced by Cladophora availability across time. The results of this study indicate that, during bloom conditions, Cladophora is the primary carbon source for both A. plicata and E. dilatata and may form the base of food webs in the upper Green River.

Nearshore and estuarine environments play a vital role in the cycling of carbon, but the effects of ocean acidification in estuarine waters have not been studied as extensively as in the open ocean. One reason for this is the limitation of pH measurement capabilities in low-salinity waters. Typically, pH in these environments has been measured using potentiometric methods that are subject to uncertainties on the order of 0.01. Spectrophotometric methods for measuring pHT offer precision and accuracy superior to those of potentiometric methods. However, previous characterizations for purified sulfonephthalein indicators, used for marine spectrophotometric measurements, are not applicable to estuarine salinities. Some estuarine datasets using unpurified indicators exist, but the presence of dye impurities affects the accuracy of these characterizations. Colorimetric impurities are known to interfere with absorbance measurements and can cause errors in pH on the order of 0.02. In this work, a mathematical model has been developed to correct spectrophotometric pHT determined with unpurified m-Cresol Purple (mCP), the indicator used most widely for these measurements. The model accounts for absorbances of colorimetric impurities that interfere with absorbance by mCP. This corrective approach brings measurements made using unpurified mCP in synthetic solutions of 0.7 M NaCl into better agreement with those made using purified mCP: within ±0.004 pH units for all six indicators tested at pHT ≤ 8.0. The model is useful for both (a) research groups currently using unpurified mCP to measure pHT, and (b) retrospective correction of historic pHT datasets collected using unpurified mCP. The correction requires only that a small sample of the unpurified mCP is saved for a single-point test at high pHT (~12), and that historic absorbance measurements are archived for subsequent correction. The principles of the corrective model were applied to an historic calibration of the mCP dissociation constant (KI) at 0 ≤ S ≤ 40 and T = 298.15 K using unpurified indicator. After correction of absorbances for dye impurities, recalculation of KI was performed, and the recalculated values were combined with mCP KI data for freshwater and seawater. The combined dataset was then refitted as a function of S and T. The resulting model is representative of mCP behavior across 0 ≤ S ≤ 40 and 278.15 ≤ T ≤ 308.15 K and produces p(KIe2) values that are within ±0.004 of p(KIe2) values from previously published purified mCP calibrations. This refitting approach was also applied to pHT determinations made with Thymol Blue (TB) and Cresol Red (CR), two sulfonephthalein indicators that have been previously used in waters outside the indicating range of mCP. The models, which were of the same form as the estuarine p(KIe2) model for mCP, performed approximately as well as the mCP model: with the exception of one high-salinity, high-temperature TB datum, all residuals were within ±0.0043 of the previously published TB and CR calibrations. Finally, an internal consistency analysis was performed using carbon chemistry data collected during two recent coastal ocean acidification research cruises. For pHT measurements performed during both cruises, purified mCP was used, and corresponding measurements of total alkalinity (TA) and dissolved inorganic carbon (DIC) were conducted. Both cruises included excursions into the Columbia River, where low salinities prevent usage of the marine p(KIe2) model for purified mCP. The Columbia River samples provided the opportunity to evaluate the internal consistency of pHT measurements made in low-salinity waters using the refitted estuarine p(KIe2) model. Although internal consistency agreement in the estuarine range is poor compared to marine measurements, pHT calculated using the new estuarine model compared well with pHT calculated using the previously published estuarine mCP model. The poor internal consistency in the estuarine range, even when making state-of-the-art pH measurements, points toward the need for a more robust characterization of the carbonic acid dissociation constants in the estuarine salinity range. This characterization should take into account the contributions of organic acids to total alkalinity in nearshore waters.

The growing crisis of antibiotic resistance is a major threat to ecosystems and human health. Infections caused by known and emerging antibiotic resistant pathogens are on the rise globally, with approximately 700,000 deaths per year caused by antibiotic resistant bacteria (1). In the United States, infections from antibiotic resistant bacteria cause more than 2 million illnesses and 23,000 deaths (2). Antibiotic resistant bacteria and antibiotic resistance genes are released into aquatic ecosystems through hospital waste, residential sewer lines and animal agricultural waste streams. Animal agriculture accounts for approximately 70% of antibiotic use in the United States (3). In agricultural ecosystems, runoff, land-applied fertilizer and waste lagoons can all contribute to the spread of antibiotic resistance. In urban ecosystems, sewage spills and other wastewater inputs contribute to the spread of antibiotic resistance. Environmental matrices, such as soil and water, can provide habitat, serving as reservoirs to potentially promote the spread of resistance. Research addressing antibiotic resistance primarily focuses on monitoring clinical occurrence and nosocomial infections (acquired in hospitals),but the natural environment also plays a role in the spread of antibiotic resistance. The consequences to aquatic ecosystems are not often studied and not well understood. Antibiotic resistance genes can transfer between bacteria through transduction, transformation and conjugation, potentially persisting in non-pathogenic environmental bacteria. Environmental reservoirs of antibiotics, antibiotic resistant bacteria and antibiotic resistance genes should be considered and integrated into frameworks to improve monitoring, regulation and management of urban and rural watersheds. The research presented in this doctoral dissertation includes field and laboratory studies designed to assess the prevalence and persistence of antibiotic resistant bacteria and antibiotic resistance genes in aquatic environments, with a focus on vancomycin-resistant enterococci, which are considered a major threat in the United States and top priority pathogens according to the Centers for Disease Control (2). The vanA gene associated with high-level resistance is located on mobile plasmids and associated with clinical infections, predominantly in the species Enterococcus faecium. E. faecium can cause bacteremia, endocarditis, pelvic infections and more (4). When vancomycin, often the last line of treatment for these infections, is no longer effective, the health burdens increase both financially and physically and infections can be fatal. Chapter 1 summarizes background and review of antibiotic resistance in the environment, including a co-authored review of culture-based methods to detect antibiotic resistant bacteria and antibiotic resistance genes in in the environment (previously published in the Journal of Environmental Quality (5). In Chapter 2, a field study was performed to investigate the occurrence and persistence of vancomycin-resistant enterococci and vanA in a sewage spill in Pinellas County, Florida, previously published in the journal Applied and Environmental Microbiology (6). In Chapter 3, antibiotic resistance genes were quantified to study their persistence in poultry litter microcosms (manuscript in prep). In Chapter 4, microcosms were used to assess how nutrients and plasmid-associated vancomycin resistance affect survival among E. faecium strains (in process of submitting for publication at Applied and Environmental Microbiology). Antibiotic resistance is a public health crisis and the results of the studies presented here contribute data towards a better understanding of environmental reservoirs of antibiotic resistant bacteria and antibiotic resistance genes. The research has broad implications for public health, environmental policy and ecosystem management.

Diatoms associated with foraminifers of the genus Amphistegina were assessed using a combination of morphological and molecular techniques. These included: 1) microscopic identification of diatoms cultured from the host, 2) sequencing of portions of the small subunit of the ribosomal RNA gene (18S) and the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase [i.e., RubisCO] gene (rbcL) from DNA extracted directly from the Amphistegina hosts and also from diatoms cultured from these hosts, and 3) denaturing gradient gel electrophoresis (DGGE) profiles of rbcL and internal transcribed spacer 1 (ITS1) PCR amplicons from DNA extracted directly from hosts and from cultures. Consistent with previous culture studies, multiple species of pennate diatoms of the genera Nitzschia, Fragilaria (including Nanofrustulum), Amphora, and Navicula, were cultured from >900 host specimens collected from >20 sites in the western Atlantic and four sites in the Pacific. Diatoms of the genus Nitzschia grew in about half of all successful cultures. The genetic identities of selected cultures were consistent with those based on morphological taxonomy. Diatom sequences from DNA extracted directly from the cytoplasm of the Amphistegina hosts were species specific and distinct from sequences obtained from cultured diatoms and from sequences in GenBank of diatom taxa previously reported as endosymbionts. Multiple phylogenetic analyses revealed that the 18S and rbcL diatom sequences from specimens of A. gibbosa collected from the Atlantic sites and of Amphistegina spp. from Hawai’i were most similar to the 18S and rbcL sequences of an unnamed Fragilariaceae diatom in GenBank (Accession # JX413542.1 for 18S and JX413559.1 for rbcL) and other closely related diatoms in that family. Of diatom taxa previously reported as endosymbionts of larger foraminifers, Nanofrustulum shiloi was the most similar, but not identical, to the sequences from hosts collected from the Atlantic and Hawai’i. The 18S and rbcL diatom sequences from the Atlantic host species, A. gibbosa, were all nearly identical, but small intra-species differences (subclades) were observed from specimens collected from the deepest (75 m) site in the Florida Keys and also from the eastern-most site, Young Island near St. Vincent. The 18S and rbcL diatom sequences from the two host species from Hawai’i, A. lobifera and A. lessonii, were more variable but still within the family Fragilariaceae. The diatom sequences from A. radiata collected from two sites in Papua New Guinea (PNG) were most similar to diatoms of the family Plagiogrammaceae and therefore distinct from sequences obtained from other Amphistegina species in this study, as well as from all diatoms previously reported as endosymbionts. A small difference was observed between the diatom sequences from host specimens collected from a Pacific site as compared to a Bismarck Sea site. The ITS1 DGGE profiles of DNA extracted directly from A. gibbosa specimens at different depths, locations, and seasons in the western Atlantic were nearly identical. Differences were seen between rbcL DGGE profiles of DNA extracted directly from the different Amphistegina host species. The rbcL DGGE profiles directly from all hosts were clearly different from those extracted from diatoms cultured from the same host specimens, as well as from Nitzschia laevis, a commonly reported diatom endosymbiont in past culture-based studies. My findings are consistent with ultrastructural studies of endosymbionts of Amphistegina published in the early 1980s and congruent with recent molecular studies of endosymbionts in other diatom-bearing foraminifers, all of which indicate specificity. Nevertheless, the consistency with which several diatom taxa have been reported in culture studies from all oceans indicates the possibility of some relationship with Amphistegina spp., either as important food items, epiphytes, or minor opportunistic symbionts that can thrive in culture media.

“Whiting” is a term used to describe a sharply defined patch of water that contains high levels of suspended, fine-grained calcium carbonate (CaCO3). These features are named for their bright (at times white) appearance when compared to surrounding waters, and have been found to occur globally, persisting for multiple consecutive days. Although whitings have been widely studied using chemical, biological, geological, and physical techniques, there has been little effort to document their spatio-temporal distributions in a systematic way, not to mention the lack of consensus on what generates whitings and allows them to persist for days to weeks at a time. In particular, although fishermen and aircraft pilots have reported whiting-like features off southwest Florida (e.g., a sighting off the Ten Thousand Islands was reported on October 29, 2013), there has been no targeted study on these features in this area. Therefore, the objective of this study is two fold: 1) to document the spatial-temporal distributions of whitings in southwest Florida (SWFL) coastal waters from 2003 through 2015 using satellite imagery to study how their occurrence is related to several environmental variables and 2) to conduct field and laboratory measurements to determine the particle composition and water characteristics in and outside the whiting features. To achieve objective one, a multi-year time series from 2003 through 2015 was developed over SWFL using Moderate Resolution Imaging Spectroradiometer (MODIS) observations. Customized processing was used in order to removed clouds and other artifacts and to delineate the surface whiting features. From this, statistics and distribution maps of whiting occurrence were generated. Annual mean whiting coverage peaked in 2011 (11 km2), when whiting reached a maximum daily visible coverage of 92 km2 on February 23. For the entire time series, the highest daily coverage observed was 126 km2 on December 6, 2008. Over all, whitings had higher spatial coverage during the spring and autumn, with 88% of all whiting coverage occurring within 40 km of the coastline. Images of average seasonal spatial distributions showed that over 90% of whitings located between 40 and 70 km of shore occurred specifically during the winter and autumn. A multivariate linear regression was performed, which found little to no correlation between annual whiting coverage and environmental factors such as sea surface temperature (SST), wind, and river discharge. This analysis was also applied to spatial distributions of whiting events within and outside of 20 km and 40 km from shore. The only statistically significant result was that of SST, as well as SST with river discharge and whiting events distributed more than 20 km from shore. In order to accomplish objective two, several field campaigns were conducted to collect in-situ data and water samples of pre-, post-, and occurring whiting event conditions to provide information on composition, driving forces, and variables that cannot be derived via satellites. Samples were collected for taxonomic identification, chemical analysis, bottom sediment grain size fractionation, in-situ remote sensing reflectance (Rrs), particle backscattering (bbp), chlorophyll-a concentration ([chl-a]), particulate absorption (ap), and gelbstoff (otherwise known as color dissolved organic matter, or CDOM) absorption (ag). Taxonomic identification of marine phytoplankton within whiting water revealed the presence of a dominant, small (<5 >μm), centric diatom species during a sampled whiting event. Through the use of scanning electron microscopy (SEM), these were identified as Thalassiosira sp. Amorphous to fully formed crystals of calcium carbonate were present, attached to cells of Thalassiosira sp., localized to the girdle bands. All other diatom species were devoid of similar growths. In comparing the waters within a whiting area to outside waters, no significant differences were found in ap, ag, nor [chl-a]. The carbonate parameters of whiting water differed from outside water, however due to low sample numbers these results are inconclusive. Average backscattering was twice as high within whiting waters compared to non-whiting water, and measured in-situ Rrs was higher at all wavelengths (400 – 700 nm) within whiting water, with a spectral shape similar to outside waters. Overall, this is the first time that SWFL whiting events have been characterized systematically using satellite imagery, field and laboratory as well as meteorological data to diagnose whiting causes and maintenance mechanisms. Although these results are inconclusive, they add new information to the existing literature on this phenomenon.

Coho salmon (Oncorhynchus kisutch) rely on unique habitats during the winter season, which may dictate how much individuals may grow and when migration from freshwater rearing habitat to the ocean occurs. Here I analyze movement timing and growth patterns for coho salmon through a field-based study and a literature review. For the field portion, I examined hatchery-stocked juvenile coho salmon across four stream basins in the Russian River watershed, California to determine the relative importance of climate, landscape, and fish size metrics in predicting movement and growth patterns over a winter rearing and spring smolt outmigration time period (December 2014-June 2015). I observed three unique movement strategies: winter parr movement, spring smolt movement, and inter-tributary movement. Movement was predicted in relation to daily temperature and precipitation, followed by in-stream and upslope basin conditions in random forest modeling. Specifically, fish that moved later were associated with basins that contained higher productivity and low-gradient floodplain habitats, while fish that moved earlier came from streams that lacked invertebrate prey and had limited low-gradient rearing habitat. Fish size and timing of movement were the primary predictors of growth, with relatively larger fish in the spring growing faster than fish that were relatively smaller prior to winter. These relationships suggest that hatchery-release fish are still highly influenced by environmental conditions once released, especially in terms of initial seasonal movement, and that watershed conditions should be considered when utilizing hatchery-rearing programs to supplement wild fish populations. In North America, coho salmon populations are distributed from Alaska through California, and may exhibit unique movement and growth patterns in relationship to population-scale vulnerability (Endangered Species Act listing), basin area, and availability and types of rearing habitat. For the second part of my thesis, I conducted a literature review to assess what factors are commonly considered in predicting movement and growth patterns for these fish, as well as the types (season and life stage) and number of movement strategies reported. Eighteen studies were summarized, of which sixteen identified unique movement strategies, ranging from one to four. Despite a wide range of basin areas and latitudes, winter parr and spring smolt movements were commonly observed, with authors primarily relating these behaviors to in-stream habitat and fish size metrics. Additionally, growth was linked positively and primarily with off-channel winter rearing, which may outweigh the importance of fish size in predicting growth when high quality rearing habitats are available during the winter season. Recognizing movement timing diversity and its drivers can help recover threatened coho salmon populations. More widely distributed populations may have unique phenotypic expressions based on localized genetic and environmental interactions, increasing diversity and overall stability across the population, a concept known as the portfolio effect. Understanding fish-habitat relationships can aid recovery efforts by providing a framework of climatic and watershed conditions that support unique behaviors, even in already severely limited populations.

Hydroscape structure can play a critical role in animal behavior, abundance, and community structure dynamics. Hydroscape configuration can be dynamic and can change quickly in ephemeral systems. However, ephemeral freshwater wetlands are among the most impacted systems in the world and restoration efforts often rely on incomplete information when establishing management objectives. Further understanding how alterations in hydroscape structure in dynamic systems affect animals is critical for conservation and management success. To determine impacts that changing hydroscape conditions can have on consumers in freshwater wetlands, I examined the effects of a large-scale physical model on fish behavior, abundance, and community structure. The physical model incorporated the restoration of sheetflow, canal-fill treatments, and the removal of a decades-old levee that divided two water management areas in the central Everglades. Small fishes modified directional movement behaviors and speed of movement before and after alterations took place, though behavioral responses varied widely by species. Density and community structure of small fishes did change as a function of canal-fill and levee removal treatments. Behaviors of large fishes were also affected by hydroscape alterations, as well as hydroscape configuration beyond the limited footprint of the physical model. Large fish abundance was altered by hydroscape alteration, particularly among certain species. Composition of the large fish community changed before and after hydroscape alteration, though magnitude of responses were site-specific. Effects of hydroscape structure proximity on trophic dynamics were examined using exclosure cages that excluded large predators but allowed access for small consumers. Exclosures were stratified according to proximity to a deep-water canal. Predator avoidance behaviors in small consumers were limited but present. Differences in behavior between sites may also be caused by differences in structure across sites and limited differences in nutrient quality. Behavioral, population, and community responses to hydroscape alteration can be valuable metrics to assess the success of hydroscape restoration. While results can vary across individuals, species, and sampling sites, effects can still be detected even at the scale of the hydroscape. My research has detailed the potential effects of restoration plans across the greater Everglades and can be extended to other ephemeral wetland restoration programs.