Cette thèse étudie par trois modèles et une expérience les effets des interactions entre le réseau vert (basé sur la production primaire) et brun (basé sur la décomposition) sur le fonctionnement des écosystèmes. Trois interactions entre les deux réseaux sont étudiées: 1) les nutriments recyclés par tous les organismes couplent les réseaux verts et bruns par une relation de mutualisme/compétition entre les producteurs primaires et les décomposeurs; 2) les consommateurs généralistes se nourrissent de proies des deux réseaux trophiques et 3) les connexions spatiales par les consommateurs généralistes mobiles en haut des réseaux trophiques et les flux de nutriments et de détritus en bas. Les résultats montrent que ces interactions peuvent affecter le fonctionnement des écosystèmes y compris les cascades trophiques, la stabilité et l'importance relative de la chaîne verte et brune. Ces résultats conduisent à (1) de nouvelles perspectives sur la modélisation du fonctionnement des réseaux trophiques, (2) des prédictions originales, (3) des nouvelles interprétations de résultats empiriques, (4) des idées sur des différences fondamentales de fonctionnement entre types d’écosystèmes, (5) des prédictions sur la réponses des écosystèmes aux changements globaux. / This thesis studies through three models and an experiment the important effects of the interactions between the green (based on primary production) and brown (based on decomposition) food webs on ecosystem functioning. Three interactions between the two food webs are studied: 1) nutrients recycled from all organisms in the food web couple the green and brown food webs through mutualistic/competitive interaction between primary producers and decomposers; 2) generalist consumers feed on prey from both food webs; and 3) the spatial connections between the two food webs through mobile generalist consumers at the top and through nutrient and detritus fluxes at the bottom of the food webs. The results show that these interactions may affect the ecosystems functioning including trophic cascades, stability and the relative importance of green and brown food chains. These results lead to new (1) insights on the way to model food webs, (2) predictions on food web functioning, (3) interpretation of empirical results, (4) ideas to compare the functioning of different ecosystem types and (5) predictions on food web responses to global changes.

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created in various seascape contexts in Abaco, Bahamas. I found that the amount of seagrass at large spatial scales was an important predictor of community assembly on these reefs. Additionally, seascape context had differing effects on various aspects of habitat quality for the most common reef species, White grunt Haemulon plumierii. The amount of seagrass at large spatial scales had positive effects on fish abundance and secondary production, but not on metrics of condition and growth. The second part of my dissertation focused on how foraging conditions for fish varied across a linear seascape gradient in the Loxahatchee River estuary in Florida, USA. Gray snapper, Lutjanus griseus, traded food quality for quantity along this estuarine gradient, maintaining similar growth rates and condition among sites. Additional work focused on identifying major energy flow pathways to two consumers in oyster-reef food webs in the Loxahatchee. Algal and microphytobenthos resource pools supported most of the production to these consumers, and body size for one of the consumers mediated food web linkages with surrounding mangrove habitats. All of these studies examined a different facet of the importance of seascape context in governing ecological processes occurring in focal habitats and underscore the role of connectivity among habitats in back-reef systems. The results suggest that management approaches consider the surrounding seascape when prioritizing areas for conservation or attempting to understand the impacts of seascape change on focal habitat patches. For this reason, spatially-based management approaches are recommended to most effectively manage back-reef systems.

Fatty acids (FAs) are used as trophic markers in aquatic food web studies, but few studies have quantified individual variability in FAs profiles over several sites in a range of conditions. I investigated whether FAs profiles of yellow perch (YP), Perca flavescens, vary with body size and between lakes with and without largemouth (Micropterus salmoides), and smallmouth bass (Micropterus dolomieu), the most common and abundant piscivores in lakes of the region. I analyzed the FAs of YP as well as zooplankton, benthic invertebrates, and prey fish collected from eight lakes where bass were either present or absent in the Outaouais region over the summer of 2016. I compared the growth rate of YP between the lakes and the YP in lakes without bass exhibited a slower growth rate. I also compared the FA signatures of YP using redundancy analysis (RDA). 23 FAs could be identified and quantified. FAs profiles were dominated by palmitic- (16:0), oleic- (18:1), stearic- (18:0), and palmitoleic acid (16:1). The RDA analysis based on FAs profiles of YP revealed variation along two main gradients (the presence of bass and the date of capture). The first two eigenvectors accounted for 42.1% of the variation (RDA1=27.6% and 2=14.6%). Arachidonic (20:4) and docosatrienoic (22:3) were the most correlated FAs with RDA1. Due to the sampling period, it was impossible to determine if the observed effects were due to the date of capture, the presence of bass, or a change in metabolism, but the last two were deemed as the most plausible explanations. It was concluded that the utility of FA signatures to quantify diet in natural environments is limited and that FAs might be more successful as markers in primary consumers and other lower trophic levels. It is recommended that a combination of FAs, stable isotopes, and modelling should be used in the future.

This study addressed a fundamental question in applied ecology and conservation; what is the predatory impact of introduced piscivorous sport fish on imperiled native fish populations? More specifically, which of many introduced species and size-classes represent the greatest threats and should be targeted for control? In order to explore this important question, an integrated analysis of stable isotopes, quantified observed diet analysis, and stable isotope mass-balance models were used to quantify trophic interactions. These tools were used to construct food web models that were then compared to draw inferences regarding the relative contribution of prey fish, including rare native fish, to the diet of introduced sport fish. The stable isotope-derived food web illustrated a slight decoupling in energy flow between a pelagic and a benthic-littoral sub-web. The quantified diet analysis suggested piscivory was low overall, and that the introduced sport fish assemblage relied heavily on zooplankton and aquatic insect prey. The integrated stable isotope and quantified diet analysis demonstrated that the consumption of prey fish, particularly pelagic prey fish, was typically underestimated using stomach content analyses. From the evaluation, comparison, and integration of food web models, I suggest that substantial predation was occurring on the early life stages of Utah Lake fishes, including native fishes, and it was not being observed using stomach content analysis. My comparative modeling demonstrated that introduced sport fish are an impediment to native fish conservation and identified the small size-class of white bass as the most immediate threat.

Large, exotic (those whose headwaters are in distant places) rivers are some of the most unique and diverse ecosystems on earth. Because they often flow through a multitude of biomes and climates, their waters are a vital resource not only for the organisms that inhabit these rivers, but for human societies as well. Thus, large rivers, like the Rio Grande, that flow through arid and agricultural regions are highly regulated and diverted. Regulation and dewatering upset a river’s natural flow regime (e.g., magnitude, duration, timing of large flood events), subsequently impacting the river’s ability to transport its sediment supply, and eventually perturbing a river into either sediment surplus or deficit. The combination of altered flow and sediment regimes influence the availability of habitat essential for the survival and viability of aquatic organisms, such as fish and invertebrates. In addition, increased deposition of sediment creates areas suitable for invasive riparian vegetation to establish, likely affecting habitat complexity and increasing the abundance of leaf litter deposited into the river. The altered flow and sediment regimes, in combination with invasive riparian vegetation, culminate and eventually affect the food resources and aquatic communities present in a river ecosystem. Most often, the links between the physical perturbations to a system with the biological factors are poorly understood. In this study, we use distinct segments of the Rio Grande along the US-Mexico border to compare areas with greater and lower habitat heterogeneity, water quality, and invasive riparian species abundance to better understand what physical factors can influence aquatic species such as fish and invertebrate communities. We identify critical limiting factors for the native fish community present, and link the altered flow and sediment regimes with the aquatic ecological template of the Rio Grande.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第17775号 / 理博第3898号 / 新制||理||1562(附属図書館) / 30582 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 中野 伸一, 准教授 奥田 昇, 教授 疋田 努 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18107号 / 理博第3985号 / 新制||理||1575(附属図書館) / 30965 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 朝倉 彰, 講師 宮崎 勝己, 教授 疋田 努 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

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<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>

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