Due to habitat degradation and overharvest (Colombo et al. 2007) sturgeon populations are declining throughout their global distribution (Pikitch et al. 2005). In North America, five sturgeon species are listed as endangered or threatened due to overharvest and habitat degradation. One species of direct concern is the pallid sturgeon (Scaphirhynchus albus ) (Boreman 1997). The morphologically similar shovelnose sturgeon (S. platorynchus) is not listed as endangered but has become a cause for concern due to poor reproductive success and declining recruitment of their offspring to the adult population, likely a result of lack of proper spawning habitat and early life foraging opportunities (Wildhaber et al. 2007). Despite listing the pallid sturgeon as endangered and increasing concern about population decline, little information is available about the foraging ecology of age–0 Scaphirhynchus sturgeon. To ensure these sturgeon populations persist in the Middle Mississippi River, a better understanding of sturgeon foraging success during early life is imperative. I quantified age–0 Scaphirhynchus sturgeon (total length (TL) range: 14–200 mm; small < 50 mm TL, large 50–200 mm TL) diets during 2004–2008 to determine whether foraging behavior changed as a function of stage height, water temperature, water velocity, size class of sturgeon, and macrohabitat. I also examined whether energy density (cal/g) and selection of prey varied across size class and macrohabitat. Age–0 Scaphirhynchus sturgeon were collected from the Middle Mississippi River during spring (March, April, May), summer (June, July, August), and fall (September, October, November). Each prey item in diets was identified to family and measured to calculate dry weight. Ephemeroptera, Diptera pupae, and Chironomidae were the dominant taxa that were consumed across all years and seasons. Large sturgeon had a broader diet, consuming more non–dominant taxa. Abiotic factors differed across macrohabitats and thus influenced foraging behavior. Sturgeon occupying the island upstream tip (IUT) macrohabitat had the largest mean mass in diet and those at the island downstream tip (IDT) had the lowest mean mass in diet. Conversely, energy density of sturgeon was highest at IDT and lowest at IUT. Small sturgeon avoided macroinvertebrates that were outside the dominant prey taxa whereas large sturgeon selected for Chironomidae across all macrohabitats. Diets of age–0 Scaphirhynchus sturgeon vary as a function of size and are influenced by interacting of abiotic and biotic factors at each macrohabitat. As age–0 Scaphirhynchus sturgeon grow, their diet broadens. Diet of young sturgeon interacts with energy condition in counterintuitive ways that requires more study. Because foraging success differs among habitats and is likely linked to recruitment, habitat quality and quantity in the Middle Mississippi River is likely critical for sturgeon population density and growth.

Knowledge of habitats used by riverine fishes throughout their life history is important for management and conservation. Naturally occurring chemical markers in otoliths have recently been used to determine natal origins and environmental history of fishes in a variety of marine and freshwater environments. However, to our knowledge no studies have examined the applicability of this technique in large floodplain rivers in United States. We evaluated otolith microchemistry and stable isotopic composition as tools for determining origins of fishes in the upper and middle Mississippi and lower Illinois Rivers, their tributaries, and associated floodplain lakes. Fishes were collected from 21 sites during summer 2006 and 2 additional sites in spring 2007. Water samples were obtained from the same 23 sites plus three additional sites during summer and fall 2006 and spring 2007. Otoliths and water samples were analyzed for δ18O, and a suite of trace elements; otoliths were also analyzed for δ13C. Tributaries, floodplain lakes, and the Illinois and Mississippi Rivers had distinct isotopic and elemental signatures. Tributaries on the Missouri and Illinois sides of the middle Mississippi River could also be differentiated by their elemental and isotopic fingerprints. Otoliths reflected differences in water chemistry among habitats. Results indicate that otolith microchemistry and stable isotope analyses provide a potentially effective means of determining origins and environmental history of fishes in large river-floodplain systems.

Insight into environments and habitats that contribute recruits to adult fish stocks in riverine systems is vital for effective population management and conservation. Catfishes are important recreational species in the Mississippi River and are commercially harvested. However, contributions from main channel and tributary habitats to catfish recruitment in large rivers such as the middle Mississippi River (between St. Louis, MO and Cairo, IL) are unknown. Stable isotope and trace elemental signatures in otoliths have been useful for determining environmental history of fishes in a variety of aquatic systems, including the Mississippi River. The objectives of this study were to identify the principle natal environments of channel catfish Ictalurus punctatus and blue catfish I. furcatus in the middle Mississippi River (MMR) using otolith stable oxygen isotopic composition (δ18O) and strontium:calcium ratios (Sr:Ca). Catfish were sampled in the MMR during July-October 2013 and 2014 and lapilli otoliths were analyzed for δ18O and Sr:Ca. Water samples from the MMR and tributaries were collected seasonally from 2006-2014 to characterize site-specific signatures. Persistent differences in water δ18O and Sr:Ca among the MMR and tributaries (including the upper Mississippi, Illinois, and Missouri rivers as well as smaller tributaries) were evident, enabling identification of natal environment for individual fish. Results indicated that blue and channel catfish stocks in the MMR primarily recruited from the largest rivers (Missouri and Mississippi rivers) in our study area and received minimal influence from smaller tributaries. Recruitment and year class strength investigations and efforts aimed at enhancing blue and channel catfish spawning and nursery habitats should be focused in the large rivers with less emphasis in the smaller tributaries.

I evaluated diet and food selection of 5 species of spring-migrating female waterfowl including 3 dabbling ducks (Blue-winged teal, Anas discors, Mallard, Anas platyrhynchos, Gadwall, Anas strepera) and 2 diving ducks (Lesser Scaup, Aythya affinis, and Ring-necked duck, Aythya collaris). Diet was evaluated with regards to the proportion of invertebrates and seeds consumed, and compared to forage availability data collected in habitats available to them at 6 study locations throughout the Upper Mississippi River and Great Lakes Region. I found latitude (i.e., stage of migration), longitude, food availability, and date all influenced the diet of spring migrating waterfowl, with some factors having a stronger influence than others. I observed differing diet trends with regard to foraging guild (e.g., dabbling and diving ducks), as each foraging guild was represented by 1 species that was heavily dependant on invertebrates (dabbling duck - Blue-winged teal; diving duck - Lesser scaup) and 1 species that was heavily dependant on seeds (dabbling duck - Mallard; diving duck - Ring-necked duck). The proportion of invertebrate foods in the diet increased throughout spring for all species of waterfowl, suggesting the importance of invertebrate food sources during spring staging. Data from this study provides valuable information to habitat managers and conservationists wishing to improve spring habitat conditions for migrating waterfowl, which likely influences waterfowl productivity.

This study utilized a new database of levee failures along 685 km of the Middle and Lower Mississippi River from St. Louis, MO to Memphis, TN during the past 120 years. The goals of this investigation were to: 1) identify the relative importance of geologic and geomorphic factors that have led to levee failures through the past century along the Mississippi River and 2) measure levee crest elevations to determine if they have increased or decreased between 1998 and 2007 and if they are built to the proper design grade elevation. Logistic regression analysis was utilized to examine selected site characteristics at each levee failure location. These site characteristics (levee failure parameters) included: 1) levee underlain by previous channel fill, 2) presence/absence of borrow pit, 3) location of failure on a meander bend, 4) width of channel, 5) width of floodway, 6) constriction-over-time factor, 7) land-cover type, 8) width of vegetative buffer, 9) sinuosity of channel, 10) intensity of dredging, and 11) presence/absence of bank revetment. Each of these parameters was evaluated using geologic maps, soil survey data, Digital Elevation Models (DEMs), historic river maps, and dredging reports (Winkley, 1977; Pinter et al., 2004). Two models were created for each river reach. The first model for both reaches used a 95% significance threshold, while the second model for the MMR used a 80% significance threshold, and the second model for the LMR used a 90% significance threshold. The first model for the Middle Mississippi River (MMR) identified only the presence/absence of channel fills to predict levee failure as significant, had an R² value of 0.178, a p-value of 0.002, and a percentage accuracy of 68.6%. The second model for the MMR identified the following variables as significant: presence/absence of channel fills to predict levee failure, location of failure on a meander bend, channel width, land-cover type, and intensity of dredging. This model had an R2 value of 0.408, p-value of 0.002, and a percentage accuracy of 74.3%. The 95% model for the Lower Mississippi River (LMR) identified location of failure on a meander bend, land-cover type, constriction-over-time factor, and sinuosity of the channel as significant. This model had an R2 value of 0.326, p-value of 0.003, and a percentage accuracy of 69.5%. The 90% LMR model identified the following variables as significant: the presence/absence of borrow pits, location of failure on meander bend, channel width, land-cover type, constriction-over-time factor, vegetative buffer width, channel sinuosity, and presence/absence of bank revetment. This model had an R2 value of 0.385, p-value of 0.006, and a percentage accuracy of 72.0%. The MMR and LMR models with the 95% significance threshold had no predictors in common because of differences between the two river reaches or possibly because of the small sample size. However, the expanded MMR and LMR models shared three predictors (i.e., meander location, channel width, and land cover type). The second portion of this project used post-processed dual-frequency GPS surveying to measure levee elevations between St. Louis, MO and Cairo, IL. These elevations were compared to the 50-year design flood grade elevations and to a 1998 DEM to identify areas of levee heightening, levee degradation and/or subsidence, and locations of past levee crevasses. This surveying revealed areas that, between 1998 and 2007, were raised up to ~1.5 meters and other areas that degraded or subsided up to ~1.0 meter. Also, the locations of five recent levee crevasses were investigated, showing local increases or decreases at those points. The importance of levee road construction type was identified through many sharp increases or decreases at the transition between road types. Overall, this project showed promising implications for the determination of levee failure susceptibility and proper levee elevation heights using logistic regression analysis and kinematic GPS surveying. The logistic regression models predicted the potential for levee failure based on local site characteristics of levees between St. Louis, MO and Memphis, TN. The high-precision kinematic GPS surveying illustrated levee elevations along the MMR to a high degree of accuracy, allowing for the rapid and efficient identification of areas that do not correspond to the proper design flood grade elevation.

Thecamoebian tests from recent lacustrine sediments have been shown to be a useful proxy to study environmental changes such as land-use changes, pollution, and climate shifts. In this study, the usefulness of thecamoebians as an environmental proxy for the Middle Mississippi River (MMR) floodplain is explored. Sediment cores and surface samples were collected from two sites in Alexander County, IL: Southern Illinois University's (SIU) MMR Wetland Field Station near East Cape Girardeau, IL and Horseshoe Lake, a dammed oxbow managed by the IL Department of Natural Resources (DNR), near Olive Branch, IL. These sites represent different floodplain environments, management histories, and flooding patterns. The thecamoebian populations were expected to reflect these differences while also responding to regional signals associated with development, agriculture, and climate. Cores were subsampled at a 5cm interval and all samples were sieved with 150μm and 45μm screens to retain thecamoebian tests. Sieved sediment was examined under a microscope and at least 100 tests were identified in each sample. Pre- and post-land clearing assemblages are recognized at each site, primarily by the increased abundance of the eutrophic-indicating species Cucurbitella tricuspis. Additionally, grab samples collected from the wetlands site during the spring indicate that the site may be influenced by road salt runoff in addition to agricultural activity. These results suggest that thecamoebians are a useful land-use change proxy and more research is needed to better understand the environmental conditions influencing assemblages.

Accurately measuring denitrification in stochastic floodplains, particularly the leveed and unleveed reaches of the Mississippi River basin, requires innovative experiments. To replicate hydraulic variability ranging from overland flooding to groundwater exfiltration in floodplain wetlands, I incubated sediment cores collected from four field sites across the Dogtooth Bend of the middle Mississippi River; pairing novel deep injection (Graphic Abstract Fig. A, left) with traditional surface delivery (Graphic Abstract Fig. A, right) of both oxic and anoxic Mississippi River water. In sandy sediments with unconstrained flux of nutrients, denitrification more than doubled across a range from 192 to 429 mg N m-2 day-1 in a linear anoxic-injection hierarchy of anoxic deep > anoxic surface > oxic deep > oxic surface treatments. In contrast, for incubations in diffusion-limited clay sediments, injection type made no difference; however, in anoxic conditions denitrification rates were as high as 435 mg N m-2 day-1 compared to oxic incubations at 187 mg N m-2 day-1. This methodology reveals the magnitude of diverse denitrification rates spanning different hydrologic conditions (Abstract Fig. B) and the mediation of denitrification by sediment type. These findings provide quantified bounds to inform resource management decisions regarding what areas should be selected for protection or hydrologic reconnection to best facilitate nutrient processing services like denitrification under varying hydrologic conditions.

In rivers that shift in their natural or modified physical structure, it is expected that organisms alter their resource use with the shifts in physical changes. The Upper Mississippi River System (UMRS) is a modified river basin and stark contrasts in both the physical structure of habitat types and biological structure in the types of organisms present exist spatially. The upper reaches of the basin contain more complex habitat types than the lower reaches which suggests resource use of fishes likely differs at least between upper and lower reaches. To date, the resource use of some commercially important, invasive, and imperiled species has been studied. However, little information regarding resource use exists for most native fishes. Understanding resource use and how it differs across time and space would benefit managers of the UMRS as programs are underway to restore and manage the system. To determine how resource use of native fishes differs spatially and temporally in the UMRS, I quantified resource use of ten native fishes across six reaches of the UMRS using multiple techniques. At the largest spatial and temporal scale, I quantified the natal origins of six prey and two predatory fishes using trace element analysis. At a seasonal scale, I quantified the collective resource use of eight species using carbon and nitrogen isotopes to compare isotopic niche space, niche overlap, and community metrics. At the shortest scale, I quantified the diets of two predatory species that are thought to compete with one another. Both large scale similarities and nuances in resource use existed in the UMRS depending on the spatial and temporal contexts. At the longest scale, fishes consistently used network connectivity as tributaries and other mainstem river reaches contributed recruits to the mainstem river. However, the percentage of individuals resulting from network connectivity and the specific rivers that lent the recruits differed among species and reaches. Particularly, large tributaries like the Minnesota and Missouri rivers contributed relatively high numbers of recruits to nearby reaches compared to other tributaries, and the most downstream reaches had the greatest contributions from network connectivity. Prey fishes recruited more often from tributaries than predators whereas consumed prey and prey collected directly from the UMRS had similar origins which were consistent across years. At a seasonal scale, breadth of resource use of individual species and the assemblage and some community metrics increased whereas overlap decreased moving downstream in the UMRS. This shift in resource use metrics coincides with shifts in the physical structure of the system. At the shortest scale, diet compositions of the two predators were similar to one another and spatially among upper reaches in the UMRS. These two predators likely coexist in part due to diet plasticity and prey size allocations that differ between species. Additionally, the relative physical homogeneity of the upper reaches of the UMRS may have led to the spatial similarity in prey use. Together, these results suggest the physical structure of the system impacted the resource use of fishes, where trophic niches and use of network connectivity shifted with the shift in physical structure of the Mississippi River. At a minimum, spatial gradients in isotopic niches and percentage of individuals coming from network connectivity suggest the resource use of fishes in downstream reaches at seasonal and life-long scales differs from the upstream reaches within this system. These differences could stem from longitudinal or functional process zone shifts in the physical structure which cannot be determined given these data. In the context of management of the system, fishes use network connectivity to at least some degree across all species and sampling reaches, indicating that the connectivity in the system should at least be maintained if not improved. Additionally, fish move among reaches (i.e., through lock and dams) and tributaries, which highlights the need for interjurisdictional management not just in the UMRS but in nearby tributary systems like the Minnesota and Missouri River where fish originated.

The lower Mississippi River alluvial valley (LMRAV) in northwestern Mississippi is characterized by a flat landscape and predominantly agricultural land use. The fluctuations in surface heat flux throughout the crop cycle due to land cover modifications are thought to have an impact on the regional weather. This research analyzes changes in convective patterns over the LMRAV based on the rapid variations in land cover as a result of the seasonal harvest cycle. Focusing on synoptically weak days between 2012-2016, data from the GOES 13-15 satellite visible imagers were used due to their 1-km spatial resolution and ability to distinguish lower clouds over a warm surface. By comparing the spatial and temporal patterns of convective clouds, the study confirmed that convective patterns do change based on land cover evolution resulting from the harvest cycle. These changes were likely a result of low-level thermal and moisture changes resulting from variations in evapotranspiration.

The Lower Mississippi Alluvial Valley (LMAV) was once the largest floodplain in the United States. Flooding regimes in the LMAV have strong impacts on the soil biogeochemical processes, nutrient cycling, forest species distribution, agricultural production, and wildlife habitat. This study characterized the LMAV flooding regimes using the 8-day-composite Moderate Resolution Imaging Spectroradiometer (MODIS) surface reflectance product from 2001 - 2018. The results showed significant spatial variations in the annual flooding duration in the LMAV, and the flooding area showed remarkable seasonal variations in the northern and central LMAV with the peak flooding area in winter and early spring. Digital Elevation Model (DEM) and slope were identified as the two major factors in determining the spatial pattern of flooding regimes. The LMAV flooding regimes dataset provides a scientific basis for the governments to design forest, agriculture, and wildlife management policies to enhance ecosystem services. Landowners also can use this information to make decisions for cropland retirement and tree plantation.