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Environmental heterogeneity in both space and time has significant repercussions for community structure and ecosystem processes. Dimictic lakes provide examples of vertically structured ecosystems that oscillate between stable and mixed thermal layers on a seasonal basis. Vertical patterns in abiotic conditions vary during both states, but with differing degrees of variation. For example, during summer thermal stratification there is high spatial heterogeneity in temperature, nutrients, dissolved oxygen and photosynthetically active radiation. The breakdown of stratification and subsequent mixing of the water column in fall greatly reduces the stability of the water column to a vertical gradient in light. Nutrients and biomass that were otherwise constrained to the depths are also suspended, leading to a boom in productivity. Freshwater lakes are teeming with microbial diversity that responds to the dynamic environment in a seemingly predictable manner. Although such patterns have been well studied for nanoplanktonic phototrophic and heterotrophic populations, less work has been done to integrate the influence of mixotrophic nutrition to the protistan assemblage. Phagotrophy by phytoplankton increases the complexity of nutrient and energy flow due to their dual functioning as producers and consumers. The role of mixotrophs in freshwater planktonic communities also varies depending on the relative balance between taxon-specific utilization of carbon and energy sources that ranges widely between phototrophy and heterotrophy. Therefore, the role of mixotrophy in the microbial food web is difficult to predict because functional types of mixotrophs along a gradient of nutritional strategies contribute differently to nutrient cycling and carbon sequestration. The overall objective of this work was to advance existing knowledge of the abundance and activity of phagotrophy phytoplankton in lacustrine systems. The incorporation of mixotrophy into the microbial food web requires the complement of physiological studies in culture (as described in chapter 2) and quantification of activity (including abundance and bacterivory) in relation to strict phototrophs and heterotrophs in situ (as described in chapter 3 and 4). Information on the physiological ecology of mixotrophic protists is crucial to understanding their role in planktonic food webs and influence on the dynamic microbial community structure in lake ecosystems. An understanding of the ecological functioning of lakes has ultimate consequences for management of water resources, particularly in the face of global climate change. / Biology

Doctor of Philosophy / Department of Geography / Melinda Daniels / Geomorphic properties of streams are linked to ecosystem function through processes related to storage, transport, and other drivers regulating biogeochemical conditions. Disturbances altering the physical template of a stream are associated with cascading impacts on ecosystem function. However, few disturbances are studied at long time scales and so the legacy of such events and the implications for ecosystem structure and function are not well understood. This research investigates the role of historic tie-driving, a channel disturbance legacy, in shaping present-day stream channel conditions in the Rocky Mountain region and the associated implications for organic matter dynamics. Using a combination of geomorphic and riparian surveys, organic matter and vegetation sampling, and modeling, I show that components of mountain stream ecosystems have recovered from tie-driving at varying rates. First, I addressed how tie-driving has altered channel morphology and wood loading. Tie-driven streams are narrower, shallower, less rough, and have less wood than non-driven reference reaches. In a second study, I focused on differences in carbon storage within the stream and riparian area between tie-driven and non-driven streams. Carbon stored on the landscape represents a long-term component of the terrestrial carbon cycle and some, but not all, components have been impacted by tie-driving. Large instream wood, coarse downed wood, and fine downed wood were identified as carbon storage components that were significantly smaller in tie-driven stream-riparian corridors. Finally, I modeled whole stream ecosystem metabolism and tested whether abiotic drivers influenced variations in rates of gross primary productivity (GPP), ecosystem respiration (ER), and net ecosystem productivity (NEP). Results from this work suggest that rates of GPP were significantly different between tie-driven and non-driven streams and were partially explained by variations in light related to canopy structure. However, variations in ER and NEP were not significantly different between tie-driven and non-driven sites. Taken as a whole, this work shows that ecosystems bear the imprint of historic disturbances but individual ecosystem components recover at differing rates. Additionally, integrating stream hydro-geomorphic and ecological dynamics is an effective approach to understanding the impact of channel disturbances in shaping ecosystem function at a variety of spatial and temporal scales.

Master of Science / Department of Biology / Craig Paukert / In-stream dredging is a common practice in rivers worldwide that can affect fish and fish habitat. We investigated the magnitude of these alterations and their influence on the fish community of the Kansas River, a large sand bed river. Fishes were collected monthly from June 2010 to June 2011 in Edwardsville and Lawrence, KS from 12, 1-km reaches (three actively dredged, two historically dredged that have not been dredged in at least one month, and seven control reaches) with bottom trawls, seines, and electrofishing. Water depths and velocities were measured with an acoustic doppler current profiler and interpolated in ArcGIS at all 12 reaches. Actively dredged reaches had proportionally more deep water habitat (> 3 m) and lower velocity (< 0.15 m/s) near the river bed than control reaches (P < 0.01 and P = 0.04, respectively). However, the mean proportion of shallow water habitat (< 0.5 m), high velocities near the river bed (> 0.30 m/s), low velocity habitat (< 0.25 m/s), and high velocity habitat (> 0.75 m/s) were similar among all reach types (Ps > 0.05). A canonical correspondence analysis was used to characterize relationships among habitat variables, reach types (actively dredged, historically dredged, and control), and catch per unit effort (CPUE) of fishes in the Kansas River. Mean velocity and depth explained a significant amount of variation in species CPUE; however, reach type was not a significant factor for any of the gear types for any season. Our results show that dredging in Great Plains Rivers can increase depths, but alterations to fish community structure was not evident, likely because many of these fishes are adapted to a range of habitat conditions and are highly mobile.

The South African National Water Act (NWA) (No. 36 of 1998) recognises that in order to sustain the goods and services that are provided by rivers and their associated biological communities, it is necessary to conserve the entire aquatic ecosystem. Conservation and maintenance of ecosystem functioning entails the protection of the biotic components (i.e. fish, macroinvertebrates, riparian vegetation, etc.) and ensuring that the abiotic driver aspects (i.e. required amount and variability of flow, water quality and fluvial geomorphology) are addressed and met (Malan and Day, 2003). According to the Reserve Determination methodology (DWAF, 2003), sustainable utilisation of the river resources requires proper, responsible management and that exploitation without understanding or limits, impacts negatively on the ecological processes, functions and communities, both in the present and the future. Manipulation of the flow regimes of rivers, to provide water when and where people need it, has resulted in a growing deterioration in the condition (health) of riverine ecosystems (King et al., 2000). Stressors on aquatic ecosystems originating from these anthropogenic activities, include point and non-point loadings, land use influences and changes, and stream modification. These are usually defined by the drivers of aquatic ecosystems namely the geomorphology, hydrology and water quality. In turn, the effects on the physical habitat and water quality have both direct and indirect effects on the biotic communities present and are usually defined by biological responses to these changes (Kleynhans et al., 2005). There is currently limited data available to formally propose a methodology to quantify the significance of altered flows in riverine ecosystems brought about by the abstraction or excessive release of water by industrial activities on a reach scale. The aim of this study was to determine the degree and magnitude of habitat-flow alterations caused by pulp and paper mill activities in the Elands and Mvoti Rivers and to link the related biological responses to them. / Prof. V. Wepener

An electrochemical sensor array can provide information about the spatial and temporal distribution of chemicals in liquid turbulent plumes. Planar laser induced fluorescence (PLIF) and amperometric sensor arrays were used to record signals from modulated chemical plumes released into a recirculating aquatic flume. Coherence analysis was applied to extract the frequency components contained in the sensor response. Effects due to release distance, modulation frequency, and array orientation were investigated. This study has demonstrated that frequency encoded information can be extracted from a turbulent chemical plume using an array of amperometric sensors with optimized three-dimensional geometry and tuning.

<p> There is a broad perception that many of the greatest knowledge gaps in marine conservation are in understanding and integrating human dimensions. Marine governance must go beyond the rhetoric that conservation will benefit from including human dimensions, and dig deeper into social science disciplines to find specific tools that may be useful. Bennett et al. (2017) advocate for &ldquo;fostering knowledge on the scope and contributions of the social sciences to conservation&rdquo; from the inception of conservation projects, during all stages of planning and implementation and at all scales, and encourage the mainstreaming of social science into conservation. However, the fractured nature of literature pointing to the importance of social science has left many unsure what is really important or what to do. This dissertation seeks to remedy this, first by mainstreaming how to strategically consider social equity, and second by learning from collective action studies. </p><p> Social equity is increasingly included in conservation mission statements &ndash; either because it is an intrinsic goal or because it is believed to have functional value to help reach other objectives. Until now, social equity has been vaguely defined, and therefore been difficult to include, monitor and evaluate in environmental governance. Chapter 1 presents a theoretical foundation for defining and distinguishing between different types of social equity and considering social equity&rsquo;s role in conservation outcomes. First, we introduce the <i>equity landscape</i> as a way to describe the distributions of resources and participation rights in a society supported by social norms in a given community. We use case studies to illustrate how environmental management can benefit from considering the equity landscape in both short- and long-term strategy. Through collaborative efforts, we also describe social equity to include several dimensions &ndash; including participation (or input to conservation interventions), and spatial, access, and financial outcomes of a conservation intervention (Klein et al. 2015). Chapter 1 motivates collecting empirical evidence of how different types of equity are experienced in a community and their influence on stakeholder behavior. </p><p> Therefore, in Chapter 2 we investigate how fishers perceive and experience these different dimensions of equity, and how different dimensions of equity influence fisher compliance with social norms and willingness to punish defectors. Our interdisciplinary approach combines a behavioral experiment and surveys, and informs important decisions on critical design elements, such as should the intervention focus on participation, or outcomes of the intervention, such as access or financial benefits? Should equity objectives be equal or fair? And, how should managers measure these objectives? This research provides important empirical insight on how equity and conservation outcomes are interlinked and how management actions may influence stakeholder cooperation, thus presenting a unique insight into equity that is applicable to a wide range of settings. </p><p> Second, this dissertation highlights the potential benefits of integrating collective action literature in fisheries management. Most problems in fisheries management are rooted in some sort of tragedy of the commons. Understanding the conditions under which cooperation can emerge and how to create policies around those conditions is extremely important for successful fisheries governance. The collective action literature contains a wealth of knowledge on how diverse types of societies can solve cooperation problems and real-world management questions. </p><p> Chapter 3 investigates two such applied questions: Do self-assembled or randomly assigned groups cooperate better? And, if there are costs to random assignment, what strategies might help offset some of these costs? We show that self-assembly and the ability to communicate face-to-face both increase compliance with rules and punishment of defectors, although self-assembly has a greater effect. </p><p> This work is specific to artisanal fishing communities in Ta&ntilde;on Strait, Philippines, but provides an approach to solving questions managers have to make on a range of key issues that likely have big consequences on conservation outcomes. By combining interdisciplinary theory and methods, my dissertation highlights how social science can both integrate into and aid conservation efforts.</p><p>

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