Master of Science / Department of Biology / Craig Paukert / I evaluated sampling strategies and the effects of dike structure modifications in the lower Missouri River to better develop sampling and mitigation strategies to protect and enhance native river fishes. Sampling occurred in the lower 1,212 km of the Missouri River during October-June (coldwater season) and June-October (warmwater season) with stationary gill nets (GN), drifted trammel nets (TN), towed otter trawls (OT), and mini fyke nets (MF) from 2003-2006. We compared probabilities of detection (p), variability (coefficient of variation; CV) in catch per unit effort, and lengths for 25 species. Over 80% of adult large-bodied fishes were collected in GN during coldwater, >90% of chub spp. (Macrhybopsis) were collected in OT, and >90% of nine small-bodied and juvenile fishes were collected in MF. Trammel nets never had the highest p during coldwater, but had the highest or equally high p for 85% of adult large-bodied fishes during warmwater. Mean CV was lowest with GN for adult large-bodied fishes; chub spp. had the lowest CV in OT. Mean lengths were typically greater in GN and TN. Large river monitoring programs might best achieve the highest p, lowest variability, and widest size range of fishes by employing GN and OT during coldwater and TN, OT, and MF during warmwater sampling periods. We also compared fish community composition and the probability an un-notched and notched dike structure and channel sand bar (referred to as channel structures) was occupied by various fish species. Few differences in species richness and diversity were evident among channel structures. Notching a dike structure had no effect on proportional abundance for any habitat guild. Catch per unit effort (CPUE) was greater at notched dikes for only three (lake sturgeon Acipenser fulvescens, paddlefish Polyodon spathula, and shovelnose sturgeon Scaphirhynchus platorynchus) of 12 great river species. Occupancy at notched dikes increased for blue catfish Ictalurus furcatus and decreased for blue sucker Cycleptus elongatus, but did not differ for 17 (81%) other species. No distinct increase in occupancy at natural channel sand bars compared to engineered dike structures was evident. Mean CPUE was higher in dike structures than channel sand bars for four great river species (goldeye Hiodon alosoides, lake sturgeon, paddlefish, and shortnose gar Lepisosteus platostomus), but did not differ for ten. Our results suggest dike structures may provide necessary habitats for many fluvial species when compared to channel sand bars, but notching did not increase abundance or occupancy of most native Missouri River fishes.

Master of Science / Department of Biology / Craig Paukert / Improperly designed stream crossings may prohibit movement of stream fishes by creating physical or behavioral barriers and may alter the form and function of stream ecosystems. A mark-recapture and geomorphological study was conducted to evaluate fish passage and stream morphology at three types of vehicle crossings (compared to control sites) located on streams in the Flint Hills of Northeast Kansas. We investigated five concrete box culverts, five low-water crossings (concrete slabs vented by one or multiple culverts), and two single corrugated culverts. A total of 6,433 fish were marked April to May 2007 and 709 were recaptured June to August 2007. Fish passage occurred at all crossing types, but upstream movement of recaptured fish was higher at controls (41.1%) than at crossing reaches (19.1%) for low-water crossings. Control sites had more species in common upstream and downstream than did crossings. There was reduced overall abundance of fish upstream at low-water crossings, commonly percids and centrarchids. A comparison of channel and road crossing dimensions showed that box culverts and corrugated culverts would be more effective than low-water crossings at transporting water, sediments, and debris during bankfull flows, and fish passage at base flows. Upstream passage of Topeka shiner (Notropis topeka), green sunfish (Lepomis cyanellus), red shiner (Cyprinella lutrensis), and Southern redbelly dace (Phoxinus erythrogaster) was tested through three simulated crossing designs (box culverts, round corrugated culverts, and natural rock) across 11 different water velocities (0.1 m/s to 1.1 m/s) in an experimental stream. Upstream movement did not differ among designs, except natural rock crossings had lower movement than box or corrugated culverts for red shiners. A greater proportion of Topeka shiners moved upstream at higher velocities. These results suggest that crossing type affects fish passage and the morphology of the stream, although water velocity in different crossing designs alone may not be a determining factor in fish passage. Low-water crossings had the greatest impact on fish community and movement, but barriers to fish movement are likely caused by other variables (e.g. perching). Use of properly designed crossing structures has great promise in conserving critical stream habitat and preserving native fish communities.

Master of Science / Department of Biology / Keith B. Gido / Nonnative species represent a major threat to the continued persistence of native fishes globally, especially in the Colorado River Basin of western North America, where there are now more nonnative than native fishes. In the upper Gila River, a tributary of the Colorado, numerous nonnative fishes have established populations, and predation by these nonnatives has been linked to extirpation of native fishes under low-flow conditions at some locations. Historically, the upper Gila lacked a top piscivore, and it is unclear what mechanisms have allowed the establishment of nonnative piscivores and resultant extension in food chain length. To investigate the phenomenon of increased food chain length through nonnative introductions we explored the influence of autochthonous energy availability on nonnative predator abundance, food chain length, and abundance of other trophic levels. Predictions were that increased basal energy availability would lead to increased nonnative predator abundance and thus increased food chain length, based upon predictions from food web theory. Annual production and biomass of four trophic levels measured across six longitudinally-positioned sites were calculated between June 2008 and June 2009 to test these predictions. In addition, energy demand of trophic levels relative to energy supply was compared across sites using a quantitative food web approach, to evaluate energy limitation across trophic levels. Primary production was found to vary considerably across the upper Gila (1,677-16,276 kcal m-2 yr-1), but production and biomass of other trophic levels was not related to this gradient as predicted. In addition, food chain length demonstrated a marginally-significant negative relationship with primary production (R[superscript]2=0.42, d.f.=5, p=0.16), which was in contrast with predicted responses. These results suggest that energy availability does not appear to be a limiting factor to the production or biomass of consumers. The influence of other mechanisms on food chain length in the upper Gila River, in particular disturbance frequency and intensity, deserve further investigation.

Master of Science / Department of Biology / Craig Paukert / We investigated spatial variation in fish assemblage and food web structure in the Kansas River, USA in relation to habitat changes. Fishes were collected at ten sites throughout the Kansas River for assessing assemblage structure in summer 2007 using fish community metrics and at 3 sites in 2006 for food web structure using stable isotope analysis. Satellite imagery indicated riparian habitat on the Kansas River was dominated by agriculture in the upper reaches (>35%) and tended to increase in urban land use in the lower reaches (>58%). Instream habitat complexity also decreased with increased urban area (<25%) becoming more channelized. Jaccard's similarity and percent similarity indices suggested that large-bodied fishes show changes in species presence and composition longitudinally within the river. Also, reaches directly above Bowersock Dam in Lawrence, Kansas and below the Johnson County Weir, near Kansas City, Kansas had low percent similarity compared to other reaches, suggesting the dam and the weir affect community composition. Canonical correspondence analysis indicated that species that prefer high velocity flows and sandy substrate (blue sucker and shovelnose sturgeon) are associated with the upper river reaches. Also, there was a higher abundance of omnivorous and planktivorous fish species in the lower more channelized river. The lower reaches contain more tolerant, macrohabitat generalist species and the upper river contained more intolerant, fluvial specialist species. Fish, macroinvertebrates, and detritus were collected at three river reaches classified as the heterogeneous instream habitat (>40% grass islands and sand bars) intermediate (22% grass islands and sand bars), and homogeneous (6% grass islands and sand bars) instream habitat reaches in June 2006. Riparian land use (proportion as agricultural and urban) was related to instream habitat with homogeneous areas having more urban riparian area compared to the heterogeneous and intermediate reaches. The heterogeneous habitat reach had higher variability in [Delta][superscript]13C for fish classified as piscivores/invertivores (P=0.029) and macroinvertebrates (P=0.004) suggesting the complex habitat in the heterogeneous habitat reach provided more variable food sources. The [Delta}15N values also indicated that ten of the twelve fish species tended to consume prey at higher trophic levels in the heterogeneous habitat reach suggesting a more complex food web. Land use practices are leading to homogenization of instream habitat and this homogenization of habitats may be related to food web diversity and trophic position of fishes. Conserving intolerant, native species in the Kansas River may require maintaining suitable habitat for these species and restoration of impacted areas of the river.

Les sols boréaux représentent l’un des plus grands stocks de carbone terrestre à l’échelle globale. Ainsi, l'un des principaux transferts de matière des écosystèmes terrestres vers les écosystèmes aquatiques concerne le transport du carbone organique. Le carbone organique dissous (COD) joue un rôle crucial dans les cycles du carbone des systèmes aquatiques boréaux, reliant les écosystèmes terrestres et aquatiques. Il constitue une source d'énergie pour les micro-organismes présents dans le sol et dans l'eau. La matière organique dissoute (MOD) dans les lacs et les sols présente diverses compositions influencées par leur source et leur temps de résidence. Elle se compose principalement de matière organique allochtone caractérisée par des composés résistants de type humique et de matière organique autochtone contenant des composés facilement dégradables de type protéique. Les processus biogéochimiques le long du continuum terre-eau boréal influencent le cycle global du carbone et, par conséquent, le climat de la Terre. Les zones riveraines (ZR) constituent des passages critiques pour le transport hydrologique latéral de la matière organique dans les écosystèmes boréaux, facilitant la connexion entre les puits de matière organique terrestres et aquatiques. Les sols riches en matières organiques des ZR sont des processeurs biogéochimiques importants dans les bassins versants, influençant considérablement la concentration et la composition de la matière organique le long du continuum terre-eau. Malgré notre compréhension du budget de carbone dans les écosystèmes terrestres et aquatiques, la transformation de la MOD le long du gradient terre-eau, en particulier aux interfaces terre-eau, demeure mal comprise.. Dans notre étude portant sur 16 bassins versants des bassins des rivières La Romaine et Eastmain des régions de la Côte-Nord et de la Baie James, respectivement, nous avons déterminé la concentration, la composition et la réactivité de la MOD dans des compartiments clés des bassins versants: le sol forestier, la ZR, les cours d'eau et les lacs. Nous avons observé des différences significatives dans la concentration et la variabilité du COD entre les compartiments du bassin versant (forêt, ZR, ruisseau, lac). Dans l'ensemble, il y a eu une diminution des concentrations et de la variabilité du COD des milieux terrestres aux milieux aquatiques, accompagnée de changements prononcés lors du passage dans la ZR. Nos recherches ont révélé le rôle central des interfaces terre-eau sur les transformations quantitatives et qualitatives de la MOD. Les diminutions rapides des concentrations totales de COD et des 4 proportions de COD dégradable pendant le passage vers les cours d'eau indiquent des pertes immédiates se produisant soit dans les cours d'eau eux-mêmes, soit par dégradation dans la ZR. Cependant, nous avons observé une présence relativement persistante de MOD d'origine terrestre dans de multiples compartiments du bassin versant. En outre, nos résultats montrent des concentrations élevées de MOD de type protéique dans les échantillons de la forêt et de la ZR, ce qui permet de mieux comprendre les sources de la MOD potentiellement terrestres de type protéique. En résumé, notre recherche met en lumière la dynamique complexe de la MOD le long des continuums terre-eau, en fournissant des informations qui améliorent notre compréhension de ces éléments vitaux au sein des écosystèmes aquatiques. / A considerable portion of the Earth's carbon is stored within boreal soils. Thus, one of the predominant transfers of mass from terrestrial to aquatic ecosystems involves the movement of organic carbon. Dissolved organic carbon (DOC) is a crucial contributor to the carbon cycles of boreal aquatic systems, linking land and water ecosystems and representing an energy source for microorganisms in both soil and water. Dissolved organic matter (DOM) in lakes and soil embodies diverse compositions influenced by their source and residence time. It predominantly consists of allochthonous DOM characterized by resistant humic-like compounds and autochthonous DOM featuring easily degradable, protein-like compounds. The biogeochemical processes along the boreal land-water gradient influence the global carbon cycle and, consequently, the Earth's climate. The riparian zones (RZ) act as critical passages for lateral hydrological transport of DOM within boreal ecosystems, facilitating the connection between diverse terrestrial DOM pools and stream DOM pools. The organic-rich soils in RZ, highlighted as biogeochemical hotspots in watersheds, significantly influence the concentration and composition of DOM along the land-water continuum. Despite our grasp of carbon budgets in terrestrial and aquatic ecosystems, the processing of DOM along the land-water gradient, particularly at land-water interfaces, remains unclear. In our study across 16 watersheds in the "La Romaine" and "Eastmain" catchments, we identified the concentration, composition, and reactivity of DOM in key watershed compartments: forest soil, RZ, streams, and lakes. We observed significant distinctions in DOM concentration and variability across watershed compartments (forest, RZ, stream, lake). Overall, there was a decrease in DOC concentrations and variability from land to aquatic environments, accompanied by abrupt shifts as it passed through the RZ. Our research revealed the pivotal role of land-water interfaces on both the quantitative and qualitative changes observed in DOM. The rapid declines in total DOC concentrations and degradable DOC proportions during the transition to streams indicate immediate losses occurring either within the streams themselves or through degradation within the RZ. However, we observed a relatively persistent presence of terrestrially derived DOM in multiple compartments within the watershed. Additionally, our finding shows high concentrations of protein-like DOM in forest and RZ samples, providing insights into the probable terrestrial sources of protein-like DOM elements. In summary, our research illuminates 6 the complex dynamics of DOM along land-water continua, enhancing our understanding our comprehension of these vital elements within aquatic ecosystems.