<p dir="ltr">Nutrients are essential to support fish production in aquatic systems but are detrimental in excess. To that end, the relationship between nutrient loading and fish biomass is hypothesized to be unimodal. In the mid-20^th century, numerous aquatic systems in North America and Europe were receiving excessive nutrients and were considered heavily degraded as a result. Since then, nutrient abatement programs have resulted in increased fish biomass in many systems throughout the two continents. However, few systems have complete records of fish biomass and nutrient loading to offer support for both sides of the unimodal fishery production curve. In Saginaw Bay, Lake Huron, total phosphorus estimates are available back to when nutrient abatement programs were first implemented in the system in the 1970s. In addition, a long-term fall bottom trawling dataset from an annual monitoring survey conducted by the Michigan Department of Natural Resources has indexed fish biomass and composition since 1970. In Chapter 2, we utilize these datasets to analyze trends in system-wide fish biomass as well as fish community trends since 1970 in response to continued nutrient abatement. We found increasing fish biomass from 1970 until the early 2000s concurrent with total phosphorus declines. However, more recently, we documented declines in system-wide fish biomass with reduced nutrient loads. We found planktivorous and benthivorous fish species displayed similar initial increases in biomass followed by more recent declines in biomass. However, we determined current total phosphorus loading was still sufficient to support piscivore biomass near peak levels.</p><p dir="ltr">While nutrients in Saginaw Bay are lower than at times in the past, the system is still highly productive. One consequence of productive systems is increased susceptibility to hypoxia, or low dissolved oxygen that can result from organic matter decomposition. Past studies have documented hypoxic conditions in Saginaw Bay in the summer and over-winter period. However, past studies have been limited in scale and have not estimated the extent or duration of hypoxia throughout the Saginaw Bay system. With climate change expected to increase the occurrence of hypoxia throughout the Laurentian Great Lakes, knowledge of dissolved oxygen dynamics in the system is becoming progressively more important. In Chapter 3, we used an array of high frequency data loggers deployed throughout inner Saginaw Bay over two summer and over-winter periods to document dissolved oxygen conditions. We also analyzed a time series dataset of bottom oxygen and environmental parameter measurements to determine the conditions that contribute to low dissolved oxygen in the bay. Further, through stable isotope analysis we investigated whether hypoxic conditions had an effect on the carbon and nitrogen (δ¹³C and δ¹⁵N) isotopic signatures of chironomid larvae, an important basal prey item in Saginaw Bay. We found instances of seasonal hypolimnetic hypoxia in the summers of 2021 and 2022 but normoxic conditions throughout the over-winter periods following each summer. We also determined bottom water and wind speed to be the most reliable predictors of low dissolved oxygen since 2011, indicating the temporary stratification that can occur during warm, calm summer periods likely precedes the development of hypoxic conditions in Saginaw Bay. Chironomid δ¹³C and δ¹⁵N values were highly variable, but some individuals displayed very low values, indicative of hypoxia exposure.</p>

An increasing number of contemporary studies in aquatic ecology emphasize the im- portance of highly unsaturated fatty acids (HUFAs) at the plant-animal interface. Studies have demonstrated a wide range of fatty acid profiles in primary producers, forcing her- bivorous zooplankton to differentially retain fatty acids to meet somatic requirements. Herbivores also vary in their somatic fatty acid profiles; cladocerans collect Eicosapen- taenoic Acid (EPA), copepods prefer Docosahexaenoic Acid (DHA). Fatty acid internal reserves can be broken down to meet structural needs (i.e. phospholipid synthesis), fuel reproduction and may play a role in cold weather adaptation. Several authors have noted increases in HUFA concentration with lowering ambient temperatures. Cladoceran membranes form a gel at lower temperatures, while copepod membranes remain fluid and allow active overwintering. Both fish and crustaceans accumulate high concentrations of HUFAs during periods of rapid growth, but colimitation with elemental resources may exist. Recent modeling results suggest food webs with high quality (nutritional and biochemical) primary producers can attain inverted biomass distributions with efficient energy transfer between trophic levels. The adoption rate for this material into man- agement studies remains low, and while other sectors of the scientific community thrive on the potential of HUFAs, planktonic food-web studies are choosing traditional view points over forward thinking. Bearing in mind the emerging hypotheses on the critical factors that drive the energy flow in the plant-animal interface, my dissertation will at- tempt to address the following general questions: What are the distinct signatures of food quality and food quantity on planktonic food web dynamics? How do nutritional and biochemical factors affect the flow of energy at the plant-animal interface? What is our current understanding of the role of highly unsaturated fatty acids (HUFAs) in aquatic food webs? To what extent can the current generation of plankton models reproduce the lower food web patterns when explicitly accounting for HUFAs? Is the integration of the HUFA role into water quality management models feasible? Explicitly accounting for HUFAs requires integrating factors of animal physiology with macro-ecology: what are the ramifications? Finally, what are the evolutionary aspects of animals coping with food quality?

An increasing number of contemporary studies in aquatic ecology emphasize the im- portance of highly unsaturated fatty acids (HUFAs) at the plant-animal interface. Studies have demonstrated a wide range of fatty acid profiles in primary producers, forcing her- bivorous zooplankton to differentially retain fatty acids to meet somatic requirements. Herbivores also vary in their somatic fatty acid profiles; cladocerans collect Eicosapen- taenoic Acid (EPA), copepods prefer Docosahexaenoic Acid (DHA). Fatty acid internal reserves can be broken down to meet structural needs (i.e. phospholipid synthesis), fuel reproduction and may play a role in cold weather adaptation. Several authors have noted increases in HUFA concentration with lowering ambient temperatures. Cladoceran membranes form a gel at lower temperatures, while copepod membranes remain fluid and allow active overwintering. Both fish and crustaceans accumulate high concentrations of HUFAs during periods of rapid growth, but colimitation with elemental resources may exist. Recent modeling results suggest food webs with high quality (nutritional and biochemical) primary producers can attain inverted biomass distributions with efficient energy transfer between trophic levels. The adoption rate for this material into man- agement studies remains low, and while other sectors of the scientific community thrive on the potential of HUFAs, planktonic food-web studies are choosing traditional view points over forward thinking. Bearing in mind the emerging hypotheses on the critical factors that drive the energy flow in the plant-animal interface, my dissertation will at- tempt to address the following general questions: What are the distinct signatures of food quality and food quantity on planktonic food web dynamics? How do nutritional and biochemical factors affect the flow of energy at the plant-animal interface? What is our current understanding of the role of highly unsaturated fatty acids (HUFAs) in aquatic food webs? To what extent can the current generation of plankton models reproduce the lower food web patterns when explicitly accounting for HUFAs? Is the integration of the HUFA role into water quality management models feasible? Explicitly accounting for HUFAs requires integrating factors of animal physiology with macro-ecology: what are the ramifications? Finally, what are the evolutionary aspects of animals coping with food quality?

Complexity science has come into the limelight in recent years as the scientific community begins to grapple with higher-order natural phenomena that cannot be fully explained via the behaviour of components at lower levels of organization. Network modeling and analysis, being a powerful tool that can capture the interconnections that embody complex behaviour, has therefore been at the forefront of complexity science. In ecology, the network paradigm is relatively young and there remain limitations in many ecological network studies, such as modeling only one type of species interaction at a time, lack of realistic network structure, or non-inclusion of community dynamics and environmental stochasticity. I introduce bioenergetic network models that bring together for the first time many of the fundamental structures and mechanisms of species interactions present in real ecological communities. I then use these models to address some outstanding questions that are relevant to understanding ecological networks at the systems level rather than at the level of subsets of interactions. Firstly, I find that realistic red-shifted environmental noise, and synchrony of species responses to noise, are associated with increased variability in ecosystem properties, with implications for predictive ecological modeling which usually assumes white noise. Next, I look at simultaneous species extinction and invasion, finding that as their individual impacts increase, their combined impact becomes decreasingly additive. In addition, the greater the impact of extinction or invasion, the lesser their reversibility via reintroduction or eradication of the species in question. For modifications of pairwise species interactions by third-party species, a phenomenon that has so far been studied one interaction at a time, I find that the many interaction modifications that occur concurrently in a community can collectively have systematic effects on total biomass and species evenness. Finally, examining a higher level of organization in the form of compartmentalized networks, I find that the relationship between intercompartment connectivity and the impacts of species decline depends considerably on network topology and whether the consumer-resource functional response is prey- or ratio-dependent. Overall, the results vary considerably across model communities with different parameterizations, underscoring the contingency and context dependence of nature that scientists and policy makers alike should no longer ignore. This work hopes to contribute to a growing multidisciplinary understanding, appreciation and management of complex systems that is fundamentally transforming the modern world and giving us insights on how to live more harmoniously within our environment.