The dissertation thesis focuses on predator ecology in artificial water bodies. Paper I deals with the importance of chemical cues for predator-prey interactions in an aquatic environment. Here, I demonstrate that the ability to detect chemical cues represents a survival benefit for prey species. Paper II points out gillnet methodological bias, which may have subsequent repercussions in field evaluation of a predator's presence and assessment of larger fish abundance in general. Papers III and IV focus on asp Leuciscus aspius spawning grounds. In Paper III, I demonstrate how males maximize their spawning chances by early arrival and in Paper IV, I evaluate the predation pressure of asp prey, Alburnus alburnus, directed on asp eggs.

This Ph.D. Thesis is focused mainly on the biology of two typical European predatory fishes, European catfish (Silurus glanis) and perch (Perca fluviatilis). Catfish is a typical apex predator, whereas perch is a smaller species that plays role of a mesopredator. Although, catfish is the third largest freshwater fish in the world, only few studies dealing with this species have been revealed thus far. The main reason is connected with capturing of the species that is inefficient by standard ichthyologic methods. Studies, that have been revealed recently, focused mainly on expansions of catfish to the West and South Europe. Catfish is unwanted in these localities due to a potential negative impact on native fish community, thus its reduction is desirable. In contrast, catfish occurrence is important in native localities where it plays a key role as a biomanipulative species (I). Catfish is a true generalist, which is a typical feature for large-bodied apex predators connected with high energy consumption of their bodies. The second typical feature is a wide diet plasticity and thus good adaptability to new food sources. It is associated with distribution of various food sources among individuals within the population (II). By contrast, perch is one of the most studied fish in the world and hundreds of studies with IF are revealed every year. However, the more information about biology of perch have been known, the more questions have been arisen. Several phenomena are revealed also in this thesis. For instance, crucial impact of juvenile perch on the entire ecosystem is described. High predation pressure on zooplankton may induce piscivory in primarily zooplanktivorous fish (III). Further, juvenile perch utilize hypoxic pelagic zones as a refuge against predation (IV). The last surprising phenomenon is described in the study dealing with both species, catfish and perch. Their coexistence may lead in strong discrimination of one species caused by special predation that was supposed to be implausible (V).

Physical factors, such as hydrologic variability, are major structuring forces of prairie stream communities. Macroinvertebrate and algae densities can both decrease sharply in response to floods and drying. Less is known about the influences of biological factors, such as fishes. The influence of fishes on macroinvertebrate communities varies with environmental factors and other biologic interactions, ranging from neutral to strong negative effects on some populations, and the strength of these interactions sometimes appear linked to hydrology. Drying intermittent streams leave permanent water refugia that may be hotspots for interactions between fishes and invertebrates. Effects of fishes on macroinvertebrate communities may vary with invertebrate life cycle stages (e.g., larvae, emerging adults, colonizing adults). I examined macroinvertebrate communities (benthic and emerging) and algal biomass across a range of permanent stream pool sites at Konza Prairie Biological Station with naturally varying densities of fishes. I also manipulated fish densities in a mesocosm experiment to address how fishes may also be effecting colonization during recovery from hydrologic disturbance. Fish biomass had a negative impact on invertebrate abundance, but not biomass or taxa richness, in natural pools. Total fish biomass was not correlated with total insect emergence in natural pools, but orangethroat darter (Etheostoma spectabile) biomass was inversely correlated with emerging Chironomidae biomass (r2 = 0.43, p = 0.047) and individual midge body size (r2 = 0.61, p = 0.014). Predatory fish biomass and a date interaction appeared in top linear models, indicating fish may also delay insect emergence from natural pools. Fish presence reduced abundance of colonizing insects (p < 0.001) and total invertebrate biomass (p = 0.001) in mesocosms. Mesocosm insect communities in pools without fishes were characterized by more Chironomidae, Culicidae, and Corduliidae (p < 0.001 for all). Chlorophyll-a increased between sampling dates in mesocosms, but did not differ between treatments. Not all life stages showed the same response to fishes, illustrating the need for understanding life histories in order to interpret the influence of fishes. Understanding how fishes in prairie streams affect ecosystem structure and function is critical for conservation and management of remaining grassland streams. Results suggest fishes can influence colonization and community structure in prairie stream pools, which serve as important refugia during hydrologic disturbance and source areas for colonists during recovery.

Worldwide declines in populations of large elasmobranchs and the potential cascading effects on marine ecosystems have garnered considerable attention. Far less appreciated are the potential ecological impacts of changes in abundances of small to medium bodied elasmobranchs mesopredators. Crucial to elucidating the role of these elasmobranchs is an understanding of their habitat use and foraging ecology in pristine conditions. I investigated the trophic interactions and factors driving spatiotemporal variation in abundances of elasmobranch mesopredators in the relatively pristine ecosystem of Shark Bay, Australia. First, I describe the species composition and seasonal habitat use patterns of elasmobranch mesopredator on the sandflats of Shark Bay. Juvenile batoids dominated this diverse community and were extremely abundant in nearshore microhabitats during the warm season. Stomach content analysis and stable isotopic analysis revealed that there is a large degree of dietary overlap between common batoid species. Crustaceans, which tend to be found in seagrass habitats, dominated diets. Despite isotopic differences between many species, overlap in isotopic niche space was high and there was some degree of individual specialization. I then, investigated the importance of abiotic (temperature and water depth) and biotic (prey and predator abundance) factors in shaping batoid habitat use. Batoids were most abundant and tended to rest in shallow nearshore waters when temperatures were high. This pattern coincides with periods of large shark abundance suggesting batoids were seeking refuge from predators rather than selecting optimal temperatures. Finally, I used acoustic telemetry to examine batoid residency and diel use of the sandflats. Individual batoids were present on the sandflats during both the warm and cold seasons and throughout the diel cycle, suggesting lower sandflat densities during the cold season were a result of habitat shifts rather than migration out of Shark Bay. Combined, habitat use and dietary results suggest that batoids have the potential to seasonally impact sandflat dynamics through their presence, although foraging may be limited on the sandflats. Interestingly, my results suggest that elasmobranch mesopredators in pristine ecosystems probably are not regulated by food supply and their habitat use patterns and perhaps ecosystem impacts may be influenced by their predators.

We test the controversial ideas about the role of corridors in fragmented animal habitats. Using simulation studies we analyze how fragmentation affects a simple prey-predator system and how the introduction of openings that connect the habitats changes the situation. Our individual based model consists of 3 levels: renewable prey food, as well as prey and predators that both have a simple economy. We find, in line with intuition, that the fragmentation of a habitat has a strong negative effect especially on the predator population. Connecting the fragmented habitats facilitates predator (and hence prey) survival, but also leads to an important counterintuitive effect: in the presence of a high quality predator, connected fragmented systems fare better in terms of coexistence than do unfragmented systems. Using a frequency domain analysis we explain how corridors between sub-habitats serve as "wave breakers" in the population flow, thus preventing deadly density waves to occur.

Rich dynamics have been demonstrated when a discrete time delay is introduced in a simple predator-prey system. For example, Hopf bifurcations and a sequence of period doubling bifurcations that appear to lead to chaotic dynamics have been observed. In this thesis we consider two different predator-prey models: the classical Gause-type predator-prey model and the chemostat predator-prey model. In both cases, we explore how different ways of modeling the time between the first contact of the predator with the prey and its eventual conversion to predator biomass affects the possible range of dynamics predicted by the models. The models we explore are systems of integro-differential equations with delay kernels from various distributions including the gamma distribution of different orders, the uniform distribution, and the Dirac delta distribution. We study the models using bifurcation theory taking the mean delay as the main bifurcation parameter. We use both an analytical approach and a computational approach using the numerical continuation software XPPAUT and DDE-BIFTOOL. First, general results common to all the models are established. Then, the differences due to the selection of particular delay kernels are considered. In particular, the differences in regions of stability of the coexistence equilibrium are investigated. Finally, the effects on the predicted range of dynamics between the classical Gause-type and the chemostat predator-prey models are compared. / Thesis / Doctor of Philosophy (PhD)

Spontaneous order happens in non-equilibrium systems composed of interacting elements. This phenomenon manifests in both the formation of space-time patterns in reaction-diffusion systems and collective rhythmic behaviors in coupled oscillators. In this thesis, we present the results of two studies: 1) The response of a multi-species predator-prey system to perturbation. 2) The features of a rich attractor space in a system of repulsively coupled Kuramoto oscillators. In the first part, we address this question: how does a complex coarsening system with non-trivial in-domain dynamics respond to perturbations? We choose a cyclic predator-prey model with six species each attacking three others. As a result of this interaction network, two competing domains form, while inside each domain three species play a rock-paper-scissors game which results in the formation of spirals inside the domains. We perturb the system by changing the interaction scheme which leads to a change of alliances and therefore a different spatial pattern. As expected, perturbing a complex space-time pattern results in a complex response. In the second part, we explore the attractor space of a system of repulsively coupled oscillators with non-homogeneous natural frequencies on a hexagonal lattice. Due to the negative coupling and the particular choice of geometry, some of the links between oscillators become frustrated. Coupled oscillators with frustration show similar features as frustrated magnetic systems. We use the parameters of the system like the coupling constant and the width of the frequency distribution to understand the system's attractor space. Further, we study the effects of external noise on the system. We also identify the breaking of time-translation invariance in the absence of external noise, in our system. / Doctor of Philosophy / Spontaneous ordering is a ubiquitous phenomenon observed in natural systems containing many interacting elements. In some systems the order is observed in the form of spatial patterns. It also can be seen in a population of coupled oscillators in the form of collective rhythmic behaviors. In this thesis, we present the results of two studies. For the first study, we choose a cyclic predator-prey system that shows a non-trivial space-time pattern. The system consists of six species each attacking three others, cyclically. By choosing such an interaction network, two competing domains form, while inside each domain three species play a rock-paper-scissors game. As a result of the inner competition, spirals form inside the domains. We study the response of the system to a perturbation. To perturb the system, we change the interaction scheme which leads to a change of alliances and therefore, a different spatial pattern. In the second study, we explore the patterns of clustering and synchronization in a system of repulsively coupled oscillators with non-homogeneous natural frequencies. Due to the negative coupling and the particular choice of geometry, some of the links between oscillators become frustrated. We use the parameters of the system such as the coupling constant and the width of the frequency distribution to understand the system’s attractor space. Further, we examine the effect of external noise on the system.

Bacteria are ubiquitous in all ecosystems and are often challenged by multiple stresses such as extreme temperatures, high salt concentrations, nutrient limitation, pH variations, radiation, predation and the presence of antibiotics/toxins. The most challenging among them is predation pressure which is one of the major causes of their mortality in different niches. Bacteria have evolved different adaptive measures to counter predation. Some of them include change in shape, size, motility, and unpalatable aggregate formation. Aromatic β-glucosides such as salicin, produced by plants as secondary metabolites, play a significant role in protecting them from herbivores. Members of the family Enterobaceriaceae primarily present in soil, e.g. Erwinia chrysanthemi (a phytopathogen) and Klebsiella aerogenes, can utilize the aromatic β-glucosides salicin and arbutin (likely to be present in soil derived from decomposing plant materials) as a carbon source unlike their fellow members such as Escherichia coli, Shigella sonnei, and Salmonella present in the gut environment. Bacteria can obtain energy by metabolizing β-glucosides in the form of glucose. Whether they can also use these molecules as defense tools in a manner similar to plants is an intriguing possibility. In such an event, Bgl+ bacteria could derive a dual advantage in terms of energy generation and protection from predation. The current study was initiated to investigate a possible link between β-glucoside metabolism and self-defense in Enterobacteriaceae. Different members of Enterobacteriaceae comprising of both laboratory strains and natural isolates were considered as prey. Predators included were laboratory strains and soil isolates of bacteriovorous nematodes of the Rhabditidae family, the amoeba Dictyostelium discoidium and a bacteriovorous Streptomyces sp. The predator-prey interaction was analyzed by performing viability and behavioral assays in the context of β-glucoside metabolism Results presented in Chapter 2 show that active catabolism of aromatic β¬glucosides like salicin, arbutin and esculin by Bgl+ bacteria decreases the viability of their predators. The aglycone products released during β-glucosides metabolism, e.g. saligenin in the case of salicin, are the causative agents of the mortality of the predators. The lethality is reversible up to a specific threshold of exposure. Saligenin acts as a chemo-attractant that lures and kills Caenorhabditis elegans N2. In the case of nematodes that succumb, bacteria can derive nutrition from the dead predators indicating a conversion of prey to predator. Experiments with mutant strains of Caenorhabditis elegans suggest that the dopaminergic receptor dop-1 is involved in mediating saligenin toxicity. Studies mentioned in Chapter 3 revolve around the relevance of the predator-prey interaction discussed in Chapter 2 in the natural environment. Members of Enterobacteriaceae and their predator amoebae (cellular slime molds) and nematodes were isolated from soil. They show coexistence in most of the soil samples analyzed. All the predators isolated from soil and other natural isolates of Caenorhabditis succumb to saligenin as their laboratory counterparts with higher sensitivity in some of the strains. Soil nematodes belonging to genera Oscheius and Mesorhabditis avoid saligenin unlike the members of Caenorhabditis genus which are attracted towards saligenin. This indicates that the soil nematodes are often exposed to saligenin or saligenin-like compounds, resulting in the evolution of a genetic machinery to avoid these toxic compounds. Studies with quasi-natural environments like soil and fruit indicate that β-glucoside metabolism have similar effects on predator prey interaction in these environments, reinforcing the relevance of these observations to the natural ecology of the organisms. The studies reported in Chapter 2 and 3 shed light on a novel defense strategy of otherwise non-pathogenic members of Enterobacteriaceae which comes with a dual advantage. These results have also brought into focus issues such as the benefit derived by bacterial populations that are genetically heterogeneous, consisting of both Bgl+ and Bgl-strains. The broad implications and future directions of the work are discussed in Chapter 4. Work presented in Appendix deals with the investigation of the pattern of cellobiose utilization in Shigella sonnei. As mentioned in Chapter 1, it is known that members of Enterobacteriaceae exhibit diversity in their pattern of β-glucoside utilization. Wild type strains of both E. coli and Shigella sonnei are unable to utilize Arbutin, Salicin and Cellobiose. While E. coli can acquire cellobiose utilizing ability directly from the wild type state (Arb-Sal-Cel-), Shigella sonnei strains, though closely related to E. coli, have to undergo a series of mutations in a specific sequence to become capable of utilizing these sugars. Characterization of a few Shigella sonnei Cel+ mutants showed a different mode of activation of the chb operon (known to be involved in cellobiose utilization in E. coli). Considering the ecological significance of the ability to hydrolyze aromatic β-glucosides, a detailed understanding of the metabolic capability of different strains and the molecular mechanism involved becomes significant.

Habitat structure modifies the strength of predator-prey interactions, but it remains unclear how to describe the three-dimensional spatial arrangement of structural components in a way that consistently predicts outcomes. Interstitial space may provide a useful target for measurement, but most studies use only two-dimensional methods to describe 3D space, limiting their predictive power. Using a novel technology to produce identical components, this study tests whether the 3D interstitial space of oyster shell mimics modifies the ability of blue crabs (Callinectes sapidus) to capture their mud crab prey (Eurypanopeous depressus) in mesocosms and a variety of reef-associated predators to capture tethered mud crabs in the field. To accomplish this, individual interstices were manipulated by changing either the orientation or internal shape of 3D printed shell mimics, representing possible ways natural oyster shells differ spatially on a reef. In mesocosms, 3D interstitial space strongly affected prey survivorship in both spatial arrangements, but striking variation in the ability of individual blue crabs to consume their prey in the Shape 1 structures was notable. Field tethering experiments mostly corroborated mesocosm findings, except in the shell shape treatment. These unexpected results were likely an artifact of differences in predation between field experiments and highlight the specificity of predator-prey interactions in structured habitats. Together, these results demonstrate that the 3D interstitial space created from the spatial arrangement of structural components can mediate predator foraging success independent of the widely studied density attribute, but these outcomes are further dependent on both predator and prey identity as well as individual variation. This study also identifies a potential target for quantifying the spatial arrangement of structural components and proposes that such a measure should be three-dimensional, capture both the size and shape of an interstice, and scaled to the specific predator-prey interaction in question.

1. Antarctic krill (Euphausia superba) form aggregations known as swarms that vary greatly in size and density. Six acoustic surveys were conducted as part of multidisciplinary studies at two study sites, the western and eastern core boxes (WCB and ECB), during the 1997, 1998 and 1999 austral summers, at South Georgia. A quantitative, automated, image processing algorithm was used to identify swarms, and calculate swarm descriptors, or metrics. In contrast to acoustic surveys of aggregations of other pelagic species, a strong correlation (r = 0.88, p = 0.02, 95% C.I.= 0.24 to 0.99) between the number of krill swarms and the mean areal krill density [rho.hat] was found. Multivariate analysis was used to partition swarms into three types, based on contrasting morphological and internal krill density parameters. Swarm types were distributed differently between inter-surveys and between on and off-shelf regions. This swarm type variation has implications for krill predators, by causing spatial heterogeneity in swarm detectability, suggesting that for optimal foraging to occur, predators must engage in some sort of adaptive foraging strategy. 2. Krill predator-prey interactions were found to occur at multiple spatial and temporal scales, in a nested, or hierarchical structure. At the largest inter-survey scale, an index of variability, I, was developed to compare variation in survey-scale predator sightings, sea temperature and [rho.hat]. Using I and a two-way ANOVA, core box, rather than year, was found to be a more important factor in determining species distribution. The absence of Blue-petrels (Halobaena caerulea) and the elevated number of Antarctic fur seals (Arctocephalus gazella) suggest that 1998 was a characterised by colder than average water surrounding South Georgia, and a high [rho.hat] in the ECB. At the smaller, intra-survey scales (<80 km, <5 day), the characteristic scale (distances in which predator group size, or krill density were similar, L_s) were determined. For krill and predators L_s varied by survey and the L_s of krill also varied by depth within a survey. Overlap in L_s were stronger between predator species than between a predator species and krill, indicating predators were taking foraging cues from the activity of predators, rather than from the underlying krill distribution. No relationship was found between swarm characteristics and predator activity, suggesting either there is no relationship between krill swarms and predators, or that the predator and acoustic observation techniques may not be appropriate to detect such a relationship. 3. To overcome the 2-D sampling limitations of conventional echosounders, a multibeam echosounder (MBE) observed entire swarms in three-dimensions. Swarms found in the nearshore environment of Livingston Island situated in the South Shetland Islands, exhibited only a narrow range of surface area to volume ratios or roughnesses (R = 3.3, CV = 0.23), suggesting that krill adopt a consistent group behaviour to maintain swarm shape. Generalized additive models (GAM) suggested that the presence of air-breathing predators influenced the shape of a krill swarm (R decreased in the presence of predators: the swarm became more spherical). A 2D distance sampling framework was used to estimate the abundance, N, and associated variance of krill swarms. This technique took into account angular and range detectability (half-normal, [sigma_r.hat] = 365.00 m, CV = 0.16) and determined the vertical distribution of krill swarms to be best approximated by a beta-distribution ([alpha.hat] = 2.62, [CV.hat] = 0.19; [beta.hat] = 2.41, [CV.hat] = 0.15), giving the abundance of swarms in survey region as [N.hat] = 5,062 ([CV.hat] = 0.35). This research represents a substantial contribution to developing estimation of pelagic biomass using MBEs. 4. When using a single- or split-beam missing pings occur when the transmit or receive cycles are interrupted, often by aeration of the water column, under the echosounder transducer during rough weather. A thin-plate regression spline based approach was used to model the missing krill data, with knots chosen using a branch and bound algorithm. This method performs well for acoustic observations of krill swarms where data are tightly clustered and change rapidly. For these data the technique outperformed the standard MGCV GAM, and the technique is applicable for estimating acoustically derived biomass from line transect surveys.