Since its introduction in 1956, the use of open-system, diel dissolved oxygen curves for estimating the components of ecosystem metabolism in the lotic setting have been important in determining the current ecosystem theory of streams, both spatially among multiple systems and longitudinally within the same system, as well as identifying potentially impaired systems, especially when contrasted with streams considered unimpaired. Several factors have been identified as controls on both components of ecosystem metabolism and include light, nutrients, and stable substrates for gross primary production (GPP) and a source of organic matter (OM) for ecosystem respiration (ER). Stream size is important at mediating these factors through the presence or absence of a riparian canopy where small streams tend to have an intact canopy that can severely limit light to primary producers but provide a good source of OM for respiration. Alternatively, larger systems tend to lose canopy cover via widening of the stream and the limitation of light is relaxed while input of OM decreases. Additionally, inputs from watershed land use can affect GPP and ER in the stream via the inputs of nutrients to stimulate algal growth or organic pollution that stimulates heterotrophic activity. In the following studies, the effect of the presence or absence of a riparian canopy, watershed land use, and stochastic events such as flooding on ecosystem metabolism in coastal plain streams of southeast Louisiana are described. These systems behave similarly to previous studies and provide more evidence that the use of ecosystem metabolism as a metric for stream health is beneficial. Recommendations for future studies include the identification of more unimpaired systems while adding a temporal component, modeling systems under different hydrologic or climate change regimes, and the assessment of the impacts of stochastic events such as extreme weather events, exotic species invasions, or local extirpations of important species.

Although on-site cryopreservation of aquatic species sperm in nitrogen-vapor shipping dewars has been used for more than 30 yr, many limitations remain. Due to the size of shipping dewars, most studies are small scale and can only produce tens of samples. The freezing temperatures that can be achieved are also affected by the size of the dewar and the number of samples being frozen due to the heat load. In addition, often due to timing or remote location these samples cannot be shipped, and if they are shipped, quality can be lost and the samples must be discarded. The goal of this thesis was to create a mobile aquatic cryopreservation laboratory that could operate at research and commercial-scale capacities and, could function under multiple scenarios in different on-site environments with a high level of quality control. There were three operational designs identified for the mobile laboratory: 1) self-contained work inside the unit using generator power; 2) work inside the unit using external facilities power; 3) using the equipment inside a host facility. Computer-aided design software was used to model a 3.8 m long trailer and various internal components to evaluate different configurations. From the final design, the layout inside the mobile laboratory was constructed and initially tested at the LSUAC Aquatic Germplasm and Genetic Resource Center. This demonstrated that the portable generator provided sufficient power for simultaneous use of all equipment. The capitol and variable costs were documented of construction and integration of the mobile laboratory into an existing cryopreservation facility at different levels of automation. This led to blueprints and layout information that can provide guidance for others to build their own units. Finally, the mobile laboratory was deployed into the field to cryopreserve sperm from Blue Catfish, Xiphophorus spp., and Red Snapper. This resulted in processing of 684 males and 6,838 French straw being produced. This work provides a general approach for high-throughput on-site cryopreservation of aquatic species for repository development and user group linkage. Germplasm repositories would allow the reconstitution of species or populations, and linking users could help remove standardization and quality control bottlenecks.

Leaf area and crown dynamics control how trees grow through their supply of carbohydrates and growth regulators, and their influence on tree mechanical stability. The influence of leaf area and crown dynamics to tree growth was investigated by testing the interdependence between leaf area, branch, and stem growth on young loblolly pine trees. The objectives were to (1) determine the influence of current and previous years leaf area on elongation of branches; (2) describe and test a unique way of quantitatively measuring the effect of neighbor branches on net growth of a target branch; (3) quantify the growth impact of reduced leaf area on selected branch whorls on stem diameter growth; and (4) describe the changes in the stem profile of young loblolly pine trees in response to different combinations of artificial defoliation and shade stress treatments. A series of shade and defoliation treatments were applied on branches on the fourth (target) whorl from the top of selected trees, considering the positional effect of branches in the crown. Ten trees were randomly assigned one of nine treatments designed to effect the carbohydrate production and growth factors on branch growth. Three levels of treatments unaltered control, foliage removed, or foliage shaded, were applied on the target branches or its upper and lower neighbors. Treatments were replicated twice in each of the five blocks in the field. Growth responses were measured from elongation of terminal leaders, diameter of branches on the target whorl, and the diameter of internodes adjacent to treated branches. Results show that elongation of terminal buds and growth of new leaves were affected by removal or shading of leaf area and the initial base diameter of the branch. The number of new fascicles, representing stem units carried on a bud, could be predicted with the length of the fully elongated bud using the power law. Growth in tree diameter was sensitive to minor changes in the leaf area of the tree crown. Stem profiles varied with reduction in leaf area of selected branches, and the effect of treatments was localized to internodes immediately above or below the branch whorls that were treated.

The Mississippi River delta is facing severe land loss. An urgent need exists to examine sediment transport and channel morphology dynamics along this highly engineered alluvial river that has shaped and will continue to shape its delta. This dissertation research focuses on investigating channel morphology dynamics and sediment transport in the recent three decades along a 327-km reach (from about 492 to 167 km upstream from the rivers outlet in the Gulf of Mexico) of the Lowermost Mississippi River (LmMR). The specific objectives of this research were to: 1) analyze riverbed adjustment, i.e., channel-bed aggradation or channel erosion at seven locations along the 327-km LmMR reach over the last three/four decades; 2) determine suspended sand availability under various discharge regimes at Tarbert Landing (the uppermost location of LmMR) during the period between 1973 and 2013; and 3) quantify bedload at Tarbert Landing, St Francisville and Baton Rouge (three uppermost locations of LmMR) and suspended load at St Francisville and Baton Rouge over the last one to four decades. This research found that the first 2025 km LmMR reach below its diversion to the Atchafalaya River and the reach from ~ 80 to 140 km experienced significant riverbed aggradation, while the reach in between (i.e. from ~ 25 to 80 km) experienced riverbed degradation over the last three/four decades. The lower 187-km reach (i.e. from 140 to 327 km) showed higher sediment outflow and negligible sediment trapping. Furthermore, the LmMR discharged an average annual sand load (SLs) of 27 million tons (MT) during 1973 and 2013, at Tarbert Landing, varying largely from 3.4 to 52.3 MT. Also, during the four decades, the LmMR at Tarbert Landing carried about 71% of the total annual sand load in about 120 days each year, when the discharge was ≥ 18000 cubic meters per second (cms). The bedload transport rates along the LmMR gradually increased from Tarbert Landing [83 million tons (MT) during 2004-2015 for grain size of 0.125 mm] to Baton Rouge (at 367.5 rk) (96 MT during 2004-2014 for the same grain size). However, the total sediment supply (bedload + suspended sediment load) was substantially higher at Tarbert Landing (931 MT) and lower and nearly equal at the other downstream locations (550 MT at St Francisville and 544 MT at Baton Rouge) during 2004-2010 (the matching period of availability for both bedload and suspended load). These findings have relevant implications for the management of river-sediment diversions along the LmMR and other large alluvial rivers in the world. They could help determine specific sediment trapping sites and the development of land building schemes.

Freshwater mussels play a vital role in their ecosystems, influencing processes such as nutrient cycling and water filtration. In addition, they provide and improve habitat for other organisms. North America is home to the most species-rich freshwater bivalve fauna in the world, but most stream systems in the U.S. have been severely degraded, and future freshwater mussel extinction rates are estimated at 6.4 percent per decade. The Pearl River Basin is a significant area of aquatic species diversity and has a complex watershed land use mosaic, providing an excellent opportunity to investigate the relative importance of local and landscape level factors on freshwater mussel assemblages. The objectives of this study were to identify freshwater mussel species richness and relative abundance in tributary streams of the Pearl River Basin, and to identify relationships between microhabitat and landscape-level environmental variables and freshwater mussel diversity in these streams. Freshwater mussel and local habitat surveys were conducted on 36 tributary streams over two summers. In addition, percent area coverage of seven land use categories and seven geology categories were estimated for each sample site. Mussel surveys revealed nine species, with total abundance ranging from 0-66 mussels per sites and species richness ranging from 0-5 species per sites. Although there were relatively few mussels at survey sites, where mussels were present, substrate composition and water chemistry appeared to be important factors influencing richness and abundance. In general, associations between local habitat variables and landscape variables were low, suggesting that local habitat features were more important in explaining mussel assemblages encountered during this study. However, other studies have documented associations between mussel assemblage characteristics and landscape scale variables. Therefore, knowledge of land use and geology should be integrated with local habitat data to accurately assess population and assemblage characteristics of these organisms in order to assist the informed development of effective management and conservation strategies for the Pearl River Basin.

Deforestation modifies otherwise intact expanses of forest into small, isolated fragments. In addition to fragmentation, deforestation also creates abrupt forest edges and large areas of regenerating vegetation where land is abandoned after clearing. Understanding how changes in the landscape affect the physical condition of birds is crucial for managing populations in human-modified landscapes. Here I use the biomarkers feather growth rate and feather quality (ptilochronology), fluctuating asymmetry (FA), and stress hormones from feathers (CORT), to estimate the physical condition of Amazonian understory birds living in forest fragments, second-growth forests, and continuous forests. Feather CORT revealed how fragmentation disrupts interspecific interactions; birds from continuous forest showed elevated hormone levels compared to birds from fragments, suggesting that reproduction and territorial behavior could be altered as a consequence of fragmentation. Fragmentation and edge effects also negatively affect the nutritional condition of birds, as shown by feather growth rate and quality over a 21-year period. Birds in fragments surrounded by young vegetation in the borders and the matrix had reduced nutritional condition compared to birds living in fragments surrounded by mature vegetation. Additionally, no indication of significant consequences of fragmentation on developmental stability were found when measuring FA in birds from forest fragments. Finally, birds living in 25 year-old second-growth forest had similar levels of nutritional condition compared to birds from continuous forest. Through the use of these biomarkers I was able to evidence some of the detrimental effects of fragmentation on the condition of birds, as well as to highlight the importance of second-growth forest vegetation in alleviating some of those detrimental effects, and in providing high-quality habitat for Amazonian understory birds. My findings support the high conservation value of second-growth forests in central Amazon, especially when allowed to regenerate for at least a few decades, as well as the importance of integrating fragments into the context of the overall landscape for the conservation and future of tropical forest biodiversity.

A range of adaptive policies is applied to the management of simulated fish stocks based on two simple models of stock dynamics, the Ricker model and the Schaefer model. Uncertainty about stock dynamics is represented as uncertainty about the parameters of these models. The policies tested include an active adaptive policy where management control options are chosen taking into account the uncertainty in the parameter estimates; a range of passive adaptive policies, where controls are chosen assuming parameter estimates are correct, but the estimates are updated from time to time; and a non-adaptive policy where the initial parameter estimates are assumed to be correct and are never updated. Analysis of the regression problems for estimating the parameters of the two models shows that a major factor determining uncertainty about parameter estimates is the variability in observed values of the independent variables in the regression. Where there is more than one independent variable, contrasts between variables are also important. Comparison of policy performances shows that the active adaptive policy always performs well relative to the optimal policy (where the true stock parameters are known). The passive adaptive policy with regular parameter estimate updating generally performs very well but occasionally very poorly. Poor performance occurs when the data points in the regression problem are clustered close to the apparent optimal levels of the independent variables. In most other cases poor initial parameter estimates cause sufficient perturbations in controls to correctly identify parameter values. The non-adaptive policy generally performs poorly, except in the case of the Ricker model where observations are available near the equilibrium stock size. This is due to the insensitivity of the optimal escapement to variations in the productivity of the stock. The good performance of the active adaptive policy is achieved at the expense of short term performance, which is sacrificed to improve parameter estimates. Infrequent updating of parameter estimates and low significance attached to new data are both shown to lead to marked deterioration in performance for the passive adaptive policy. The major conclusion from the cases studied is that good estimation (equivalent to good understanding about stock dynamics) and hence good policy performance requires sufficient variability in, and contrasts between, the independent variables in the corresponding regression problems. It is suggested that this conclusion can be extended to more general problems of uncertainty about system dynamics in managing renewable resources provided that the problems can be simplified to an understanding of the key processes and uncertainties involved. The quantities corresponding to independent variables in an appropriate regression problem can then be identified and appropriate experimental management strategies devised to discriminate between alternative hypotheses. / Science, Faculty of / Zoology, Department of / Graduate

Louisiana estuaries provide habitat for some of the most productive population of the eastern oyster, Crassostrea virginica in the Gulf of Mexico. Coastal alterations, including changes in river flow of the Mississippi River, sediment diversions, and climate change, are likely to impact areas supporting oyster production. Although oysters in Louisiana already experience periods of high total suspended sediment, these coastal alterations may increase duration, frequency, and concentration of high suspended sediment concentrations over oyster grounds, which could have significantly impact oyster physiology and production by affecting basic physiological functions of oysters. In this study, we measured effects of acute (1 hour) and chronic (8 weeks) exposure of suspended sediment concentrations on eastern oyster physiology. Specifically, using a series of controlled laboratory experiments, we monitored oyster respiration rate (O2 L-1 hr-1 g-1 dry tissue weight) and clearance rate (L hr-1 g-1 dry tissue weight) in response to acute and chronic exposure to suspended sediment concentrations. Acute exposure at six sediment concentrations (0, 10, 50, 200, 500, 1000 mg L-1) indicated sediment concentration significantly affected oyster clearance rates (p < 0.0001), but not respiration rates (p = 0.12). Chronic exposure at two salinities (6 and 15 ppt) and three sediment concentrations (0, 50, 400 mg L-1) indicated that clearance rates were not significantly affected by sediment concentration or salinity (p = 0.71 and p = 0.86 respectively). Respiration rate was not significantly affected by sediment concentration (p = 0.21) but was significantly affected by salinity (p = 0.0086). Overall, reduced salinity associated with sediment diversions may have greater impacts on oyster growth and survival, particularly if salinities are reduced for extended periods of time. Understanding consequences of high suspended sediment exposure on the eastern oyster is critical to predicting future oyster production potential, impacts from proposed restoration activities, and climate change.

Since 1986, Louisianas American alligator (Alligator mississippiensis) ranching program has required the release of alligators produced from eggs collected from wild nests to maintain wild populations. This project assessed long-term harvest data (1991-2010s) to estimate survival of released alligators. First, wildlife and fishery harvest models and general inter-disciplinary survival models were evaluated to determine best fit to the data. Second, once the best fitting model was selected, release length, precipitation and temperature from release sites, and an index of hunter effort were added to investigate influences on survival estimates. Release length was included because over time the proportion and size of ranch-released alligators has been modified. The generalized linear mixed model, with a fixed intercept, and negative binomial probability distribution was selected as the best fitting model based on the minimization of differences between observed and expected values. This baseline model without covariates estimated instantaneous annual survival to be 0.87 and 0.89, for male and female alligators, respectively. The final best fitting model suggested that the larger an alligator is at release (to a certain point, benefits diminishing after 139 cm), the higher the chance of survival, and the longer it will be afield, for both males (F_1,169=5.62, p<0.05) and females (F_1,180=5.89, p<0.05). Mean precipitation was also statistically significant and positively associated with survival of both male (F_1,169=12.51, p<0.05) and female (F_1,180=12.33, p<0.05) alligators, suggesting reduced survival in drier years. Additionally, for male alligators, the coefficient of variation for mean temperature was statistically significant (F_1,169=7.19, p<0.05), suggesting lowered survival during years with more variation in temperature between months. Although not statistically significant, fit of the male model improved with the inclusion of the hunter effort covariate. Inclusion of release length along with environmental and hunter effort covariates improved precision of survival estimates resulting in values of 0.79 for males, and 0.81 for females, suggesting survival was influenced by the included covariates. Survival estimates with included environmental variables were very similar to reported wild alligator survival estimates, suggesting that ranch-released alligators respond to environmental conditions similar to wild alligators and that ranch-released alligator estimates may provide insights into wild alligator ecology.

Weak biotic responses to habitat gradients within Northern Gulf of Mexico streams have been attributed to spatial and temporal variability. Landscape and in-stream habitat descriptions are presented for watersheds within Pleistocene terraces of the Coastal Plains geomorphic province of Louisiana, USA. Geologic influences on stream habitat were inferred by comparing multivariate ordinations on physicochemical measurements between terraces. Seasonal variability was assessed during a drought year (2011) and a typical water year (2013). Within coastal plains of Louisiana, stream condition was more similar within terraces than within river basins. Permutational MANOVA models indicated significantly different stream habitat between Uplands and Prairie, with intermediate habitat in Flatwoods. Seasonal differences were detected more frequently during normal flow condition, suggesting that baseflow impacts habitat heterogeneity between adjacent terraces. Macroinvertebrates were collected throughout a drought year at stream sites stratified among coastal plain terraces to quantify spatial and temporal variability and identify functional habitat gradients. Macroinvertebrate assemblages differed between Uplands and Prairie terraces, especially regarding insect taxa, which were associated with better water quality and structurally complex habitat. Drought and other disturbances selected against lotic taxa expected in the intermediate Flatwoods terrace. Widening the lateral scope of the study landscape helped identify habitat thresholds and define regional habitat preference of individual taxa. Aquatic habitat improvement in Prairie terrace bayous should include restoring baseflow, increasing structural complexity and protecting macroinvertebrate source populations in the Uplands. Aquatic insect larvae are important bio-indicators and flexible life histories of many taxa may reflect regional or seasonal variability in environmental conditions. Larval development and reproductive strategy inferred from seasonal size distributions are presented for specimens of Caenis sp. (Ephemeroptera: Caenidae) in the coastal plain terraces of Louisiana. Influence of regional drought, landscape features and water quality on growth rate, terminal size and voltinism are examined. Caenis sp. in subtropical Louisiana exhibited bivoltine emergences in November and July. Size at instar development class did not differ by terrace, but was influenced by local water quality (e.g., orthophosphate concentration, specific conductance and biochemical oxygen demand). Maintenance of baseflow during drought enhanced abundance of Caenis larvae in streams with chronic disturbance from agriculture.